Parameters Input values
Folder name : Example data
Sequence name : CDH1
Group : High methylated DNA
Experiment type : Direct-BSP
Replicate number : 3
Date of sequencing #1 : 2022-05-02
Date of sequencing #2 : 2022-05-02
Date of analysis : 2023-06-09 17:23
Prefix of output files : CDH1_High methylated DNA_3

Reference DNA

Reference DNA sequence

Reference DNA sequence information Input values
Name CDH1
Strand used for primer design Plus strand
Length 341 pb
Coordinates on reference genome chr16:68770940-68771280

Genomic DNA Sequence from plus strand (template strand):

## CCACCGGCGGGGCTGGGATTCGAACCCAGTGGAATCAGAACCGTGCAGGTCCCATAACCCACCTAGACCCTAGCAACTCCAGGCTAGAGGGTCACCGCGTCTATGCGAGGCCGGGTGGGCGGGCCGTCAGCTCCGCCCTGGGGAGGGGTCCGCGCTGCTGATTGGCTGTGGCCGGCAGGTGAACCCTCAGCCAATCAGCGGTACGGGGGGCGGTGCCTCCGGGGCTCACCTGGCTGCAGCCACGCACCCCCTCTCAGTGGCGTCGGAACTGCAAAGCACCTGTGAGCTTGCGGAAGTCAGTTCAGACTCCAGCCCGCTCCAGCCCGGCCCGACCCGACCGC

Genomic DNA Sequence from minus strand (not used):

## GCGGTCGGGTCGGGCCGGGCTGGAGCGGGCTGGAGTCTGAACTGACTTCCGCAAGCTCACAGGTGCTTTGCAGTTCCGACGCCACTGAGAGGGGGTGCGTGGCTGCAGCCAGGTGAGCCCCGGAGGCACCGCCCCCCGTACCGCTGATTGGCTGAGGGTTCACCTGCCGGCCACAGCCAATCAGCAGCGCGGACCCCTCCCCAGGGCGGAGCTGACGGCCCGCCCACCCGGCCTCGCATAGACGCGGTGACCCTCTAGCCTGGAGTTGCTAGGGTCTAGGTGGGTTATGGGACCTGCACGGTTCTGATTCCACTGGGTTCGAATCCCAGCCCCGCCGGTGG

Localization of CG dinucleotides

CG positions on plus strand

CG number chr start end C position G position
1 chr16 68770944 68770945 5 6
2 chr16 68770947 68770948 8 9
3 chr16 68770960 68770961 21 22
4 chr16 68770981 68770982 42 43
5 chr16 68771035 68771036 96 97
6 chr16 68771037 68771038 98 99
7 chr16 68771045 68771046 106 107
8 chr16 68771051 68771052 112 113
9 chr16 68771059 68771060 120 121
10 chr16 68771064 68771065 125 126
11 chr16 68771073 68771074 134 135
12 chr16 68771090 68771091 151 152
13 chr16 68771092 68771093 153 154
14 chr16 68771112 68771113 173 174
15 chr16 68771138 68771139 199 200
16 chr16 68771143 68771144 204 205
17 chr16 68771150 68771151 211 212
18 chr16 68771159 68771160 220 221
19 chr16 68771182 68771183 243 244
20 chr16 68771200 68771201 261 262
21 chr16 68771203 68771204 264 265
22 chr16 68771230 68771231 291 292
23 chr16 68771254 68771255 315 316
24 chr16 68771264 68771265 325 326
25 chr16 68771269 68771270 330 331
26 chr16 68771274 68771275 335 336
27 chr16 68771278 68771279 339 340

CG positions on minus strand

CG number chr start end C position G position
27 chr16 68771278 68771279 2 3
26 chr16 68771274 68771275 6 7
25 chr16 68771269 68771270 11 12
24 chr16 68771264 68771265 16 17
23 chr16 68771254 68771255 26 27
22 chr16 68771230 68771231 50 51
21 chr16 68771203 68771204 77 78
20 chr16 68771200 68771201 80 81
19 chr16 68771182 68771183 98 99
18 chr16 68771159 68771160 121 122
17 chr16 68771150 68771151 130 131
16 chr16 68771143 68771144 137 138
15 chr16 68771138 68771139 142 143
14 chr16 68771112 68771113 168 169
13 chr16 68771092 68771093 188 189
12 chr16 68771090 68771091 190 191
11 chr16 68771073 68771074 207 208
10 chr16 68771064 68771065 216 217
9 chr16 68771059 68771060 221 222
8 chr16 68771051 68771052 229 230
7 chr16 68771045 68771046 235 236
6 chr16 68771037 68771038 243 244
5 chr16 68771035 68771036 245 246
4 chr16 68770981 68770982 299 300
3 chr16 68770960 68770961 320 321
2 chr16 68770947 68770948 333 334
1 chr16 68770944 68770945 336 337

Bisulfite converted sequences

Converted sequence sense (template strand)

Bisulfite converted sequence of the plus strand as indicated as the template strand.

## TTATCGGCGGGGTTGGGATTCGAATTTAGTGGAATTAGAATCGTGTAGGTTTTATAATTTATTTAGATTTTAGTAATTTTAGGTTAGAGGGTTATCGCGTTTATGCGAGGTCGGGTGGGCGGGTCGTTAGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTTGCGGAAGTTAGTTTAGATTTTAGTTCGTTTTAGTTCGGTTCGATTCGATCGT

Converted sequence antisense (reverse complement)

Reverse complement of the bisulfite converted sequence from the plus strand.

## ACGATCGAATCGAACCGAACTAAAACGAACTAAAATCTAAACTAACTTCCGCAAACTCACAAATACTTTACAATTCCGACGCCACTAAAAAAAAATACGTAACTACAACCAAATAAACCCCGAAAACACCGCCCCCCGTACCGCTAATTAACTAAAAATTCACCTACCGACCACAACCAATCAACAACGCGAACCCCTCCCCAAAACGAAACTAACGACCCGCCCACCCGACCTCGCATAAACGCGATAACCCTCTAACCTAAAATTACTAAAATCTAAATAAATTATAAAACCTACACGATTCTAATTCCACTAAATTCGAATCCCAACCCCGCCGATAA

Sequencing trimming

Summary

Thresholds Values
Minimum length of the trimmed sequence : 30 bp
Minimum Phred quality score : 30
Minimum ratio of primary peak : 0.75
Minimum percentage of non-mixed positions : 75 %
Sequencing Length Start position End position Mean of Phred quality scores Mean of primary peak ratio Percentage of non-mixed positions Trimmed sequence quality
#1 205 27 231 46.68 0.94 89.27 Correct
#2 207 7 213 42.54 0.96 94.20 Correct

Sequencing result #1

Raw sequence

Sequence

Sequence of primary peaks:

Length: 244 bp 

## TAATAAGGGGTAATTATGGGTTGAGGGTTTTGCGTTGTGCGAAGGGCGGGTGGGCGGGCCGTTGGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTTCCTCGACTGTGCCTTCTAAA
Chromatogram

Open chromatogram file in a new tab

Table
Position A peak T peak G peak C peak Total A ratio T ratio G ratio C ratio Primary base Quality score Primary ratio
1 3 61 0 0 64 0.05 0.95 0.00 0.00 T 13 0.95
2 7 0 0 0 7 1.00 0.00 0.00 0.00 A 14 1.00
3 19 0 0 0 19 1.00 0.00 0.00 0.00 A 10 1.00
4 0 29 0 0 29 0.00 1.00 0.00 0.00 T 13 1.00
5 14 0 0 0 14 1.00 0.00 0.00 0.00 A 13 1.00
6 14 0 0 0 14 1.00 0.00 0.00 0.00 A 8 1.00
7 0 0 176 0 176 0.00 0.00 1.00 0.00 G 10 1.00
8 0 0 211 0 211 0.00 0.00 1.00 0.00 G 14 1.00
9 0 0 132 0 132 0.00 0.00 1.00 0.00 G 9 1.00
10 0 0 113 0 113 0.00 0.00 1.00 0.00 G 14 1.00
11 0 17 0 0 17 0.00 1.00 0.00 0.00 T 3 1.00
12 2249 0 776 0 3025 0.74 0.00 0.26 0.00 A 8 0.74
13 4167 0 0 0 4167 1.00 0.00 0.00 0.00 A 8 1.00
14 4791 12799 0 0 17590 0.27 0.73 0.00 0.00 T 15 0.73
15 0 12600 0 0 12600 0.00 1.00 0.00 0.00 T 17 1.00
16 14 0 0 0 14 1.00 0.00 0.00 0.00 A 22 1.00
17 0 9598 0 0 9598 0.00 1.00 0.00 0.00 T 20 1.00
18 0 0 3 0 3 0.00 0.00 1.00 0.00 G 12 1.00
19 0 0 4132 0 4132 0.00 0.00 1.00 0.00 G 20 1.00
20 4 5 4779 0 4788 0.00 0.00 1.00 0.00 G 22 1.00
21 0 4608 0 0 4608 0.00 1.00 0.00 0.00 T 16 1.00
22 2759 4002 0 0 6761 0.41 0.59 0.00 0.00 T 5 0.59
23 0 0 946 0 946 0.00 0.00 1.00 0.00 G 5 1.00
24 3989 0 0 0 3989 1.00 0.00 0.00 0.00 A 20 1.00
25 0 0 3676 0 3676 0.00 0.00 1.00 0.00 G 30 1.00
26 6 0 5006 0 5012 0.00 0.00 1.00 0.00 G 30 1.00
27 0 2 2368 0 2370 0.00 0.00 1.00 0.00 G 33 1.00
28 2 2342 2 0 2346 0.00 1.00 0.00 0.00 T 20 1.00
29 1619 1818 0 0 3437 0.47 0.53 0.00 0.00 T 17 0.53
30 0 2202 0 0 2202 0.00 1.00 0.00 0.00 T 17 1.00
31 3 1323 0 580 1906 0.00 0.69 0.00 0.30 T 16 0.69
32 0 0 2518 0 2518 0.00 0.00 1.00 0.00 G 26 1.00
33 0 0 0 627 627 0.00 0.00 0.00 1.00 C 34 1.00
34 0 0 931 0 931 0.00 0.00 1.00 0.00 G 35 1.00
35 0 1617 0 0 1617 0.00 1.00 0.00 0.00 T 34 1.00
36 0 1901 3 0 1904 0.00 1.00 0.00 0.00 T 29 1.00
37 1579 0 2296 0 3875 0.41 0.00 0.59 0.00 G 24 0.59
38 0 1177 0 0 1177 0.00 1.00 0.00 0.00 T 27 1.00
39 0 1 796 0 797 0.00 0.00 1.00 0.00 G 16 1.00
40 610 0 0 707 1317 0.46 0.00 0.00 0.54 C 16 0.54
41 0 0 786 1 787 0.00 0.00 1.00 0.00 G 27 1.00
42 712 192 0 0 904 0.79 0.21 0.00 0.00 A 22 0.79
43 497 0 364 0 861 0.58 0.00 0.42 0.00 A 14 0.58
44 0 607 871 0 1478 0.00 0.41 0.59 0.00 G 12 0.59
45 0 0 2 0 2 0.00 0.00 1.00 0.00 G 21 1.00
46 0 0 2 0 2 0.00 0.00 1.00 0.00 G 18 1.00
47 0 349 1 860 1210 0.00 0.29 0.00 0.71 C 19 0.71
48 0 2 979 2 983 0.00 0.00 1.00 0.00 G 26 1.00
49 0 130 715 0 845 0.00 0.15 0.85 0.00 G 35 0.85
50 0 0 757 0 757 0.00 0.00 1.00 0.00 G 29 1.00
51 0 428 0 0 428 0.00 1.00 0.00 0.00 T 27 1.00
52 202 0 797 0 999 0.20 0.00 0.80 0.00 G 26 0.80
53 0 0 696 0 696 0.00 0.00 1.00 0.00 G 36 1.00
54 0 172 388 0 560 0.00 0.31 0.69 0.00 G 33 0.69
55 0 129 0 664 793 0.00 0.16 0.00 0.84 C 36 0.84
56 0 0 730 282 1012 0.00 0.00 0.72 0.28 G 25 0.72
57 0 1 741 349 1091 0.00 0.00 0.68 0.32 G 15 0.68
58 0 285 304 0 589 0.00 0.48 0.52 0.00 G 14 0.52
59 0 462 1 467 930 0.00 0.50 0.00 0.50 C 14 0.50
60 1 0 0 981 982 0.00 0.00 0.00 1.00 C 26 1.00
61 192 0 489 0 681 0.28 0.00 0.72 0.00 G 26 0.72
62 0 302 1 148 451 0.00 0.67 0.00 0.33 T 15 0.67
63 0 1241 1 1 1243 0.00 1.00 0.00 0.00 T 26 1.00
64 444 0 542 0 986 0.45 0.00 0.55 0.00 G 15 0.55
65 0 187 658 0 845 0.00 0.22 0.78 0.00 G 25 0.78
66 0 483 226 0 709 0.00 0.68 0.32 0.00 T 16 0.68
67 0 994 2 337 1333 0.00 0.75 0.00 0.25 T 16 0.75
68 0 772 0 0 772 0.00 1.00 0.00 0.00 T 40 1.00
69 0 416 0 994 1410 0.00 0.30 0.00 0.70 C 29 0.70
70 0 0 327 2 329 0.00 0.00 0.99 0.01 G 25 0.99
71 0 422 0 308 730 0.00 0.58 0.00 0.42 T 16 0.58
72 1 1294 0 0 1295 0.00 1.00 0.00 0.00 T 26 1.00
73 589 703 0 0 1292 0.46 0.54 0.00 0.00 T 15 0.54
74 622 921 1 0 1544 0.40 0.60 0.00 0.00 T 15 0.60
75 0 3 1242 0 1245 0.00 0.00 1.00 0.00 G 26 1.00
76 46 0 404 0 450 0.10 0.00 0.90 0.00 G 51 0.90
77 0 0 630 0 630 0.00 0.00 1.00 0.00 G 51 1.00
78 2 0 644 0 646 0.00 0.00 1.00 0.00 G 29 1.00
79 893 0 0 0 893 1.00 0.00 0.00 0.00 A 29 1.00
80 1 0 668 0 669 0.00 0.00 1.00 0.00 G 46 1.00
81 1 0 970 0 971 0.00 0.00 1.00 0.00 G 58 1.00
82 0 0 798 0 798 0.00 0.00 1.00 0.00 G 61 1.00
83 0 0 726 0 726 0.00 0.00 1.00 0.00 G 61 1.00
84 0 756 0 0 756 0.00 1.00 0.00 0.00 T 61 1.00
85 0 914 0 0 914 0.00 1.00 0.00 0.00 T 61 1.00
86 0 3 2 1071 1076 0.00 0.00 0.00 1.00 C 58 1.00
87 0 0 652 0 652 0.00 0.00 1.00 0.00 G 58 1.00
88 0 0 4 807 811 0.00 0.00 0.00 1.00 C 58 1.00
89 0 0 1138 0 1138 0.00 0.00 1.00 0.00 G 58 1.00
90 0 799 3 0 802 0.00 1.00 0.00 0.00 T 58 1.00
91 0 854 0 0 854 0.00 1.00 0.00 0.00 T 58 1.00
92 0 3 1047 0 1050 0.00 0.00 1.00 0.00 G 51 1.00
93 0 605 2 0 607 0.00 1.00 0.00 0.00 T 58 1.00
94 0 912 2 0 914 0.00 1.00 0.00 0.00 T 58 1.00
95 0 2 1004 0 1006 0.00 0.00 1.00 0.00 G 58 1.00
96 842 1 2 0 845 1.00 0.00 0.00 0.00 A 58 1.00
97 1 696 0 0 697 0.00 1.00 0.00 0.00 T 51 1.00
98 0 958 1 0 959 0.00 1.00 0.00 0.00 T 51 1.00
99 0 4 1226 0 1230 0.00 0.00 1.00 0.00 G 41 1.00
100 0 2 565 0 567 0.00 0.00 1.00 0.00 G 51 1.00
101 0 518 0 0 518 0.00 1.00 0.00 0.00 T 51 1.00
102 0 957 3 0 960 0.00 1.00 0.00 0.00 T 51 1.00
103 0 5 1344 0 1349 0.00 0.00 1.00 0.00 G 58 1.00
104 0 530 0 0 530 0.00 1.00 0.00 0.00 T 61 1.00
105 0 2 1294 0 1296 0.00 0.00 1.00 0.00 G 61 1.00
106 0 2 675 0 677 0.00 0.00 1.00 0.00 G 51 1.00
107 0 479 0 1 480 0.00 1.00 0.00 0.00 T 58 1.00
108 0 2 0 991 993 0.00 0.00 0.00 1.00 C 51 1.00
109 0 0 659 2 661 0.00 0.00 1.00 0.00 G 58 1.00
110 0 0 757 0 757 0.00 0.00 1.00 0.00 G 51 1.00
111 2 421 1 0 424 0.00 0.99 0.00 0.00 T 51 0.99
112 733 1 1 0 735 1.00 0.00 0.00 0.00 A 51 1.00
113 0 0 435 0 435 0.00 0.00 1.00 0.00 G 46 1.00
114 0 2 845 0 847 0.00 0.00 1.00 0.00 G 58 1.00
115 0 524 0 0 524 0.00 1.00 0.00 0.00 T 58 1.00
116 4 0 871 0 875 0.00 0.00 1.00 0.00 G 58 1.00
117 840 0 2 0 842 1.00 0.00 0.00 0.00 A 58 1.00
118 657 0 0 0 657 1.00 0.00 0.00 0.00 A 58 1.00
119 1 758 0 0 759 0.00 1.00 0.00 0.00 T 46 1.00
120 0 1165 0 0 1165 0.00 1.00 0.00 0.00 T 51 1.00
121 0 962 0 0 962 0.00 1.00 0.00 0.00 T 51 1.00
122 0 906 0 0 906 0.00 1.00 0.00 0.00 T 58 1.00
123 0 759 0 0 759 0.00 1.00 0.00 0.00 T 61 1.00
124 849 2 2 0 853 1.00 0.00 0.00 0.00 A 58 1.00
125 0 2 620 0 622 0.00 0.00 1.00 0.00 G 58 1.00
126 0 639 0 0 639 0.00 1.00 0.00 0.00 T 51 1.00
127 3 808 0 0 811 0.00 1.00 0.00 0.00 T 58 1.00
128 639 2 0 0 641 1.00 0.00 0.00 0.00 A 51 1.00
129 547 2 0 0 549 1.00 0.00 0.00 0.00 A 51 1.00
130 2 685 0 0 687 0.00 1.00 0.00 0.00 T 51 1.00
131 2 957 0 0 959 0.00 1.00 0.00 0.00 T 51 1.00
132 792 3 2 0 797 0.99 0.00 0.00 0.00 A 51 0.99
133 3 0 693 0 696 0.00 0.00 1.00 0.00 G 58 1.00
134 0 0 0 528 528 0.00 0.00 0.00 1.00 C 58 1.00
135 0 0 880 2 882 0.00 0.00 1.00 0.00 G 58 1.00
136 0 0 566 0 566 0.00 0.00 1.00 0.00 G 58 1.00
137 2 534 1 0 537 0.00 0.99 0.00 0.00 T 51 0.99
138 655 0 0 0 655 1.00 0.00 0.00 0.00 A 51 1.00
139 1 0 1 599 601 0.00 0.00 0.00 1.00 C 41 1.00
140 0 0 482 0 482 0.00 0.00 1.00 0.00 G 58 1.00
141 0 0 879 0 879 0.00 0.00 1.00 0.00 G 58 1.00
142 0 0 583 0 583 0.00 0.00 1.00 0.00 G 58 1.00
143 0 0 685 0 685 0.00 0.00 1.00 0.00 G 58 1.00
144 0 0 722 0 722 0.00 0.00 1.00 0.00 G 58 1.00
145 0 0 716 2 718 0.00 0.00 1.00 0.00 G 61 1.00
146 0 0 4 536 540 0.00 0.00 0.01 0.99 C 61 0.99
147 0 0 872 2 874 0.00 0.00 1.00 0.00 G 58 1.00
148 0 0 679 0 679 0.00 0.00 1.00 0.00 G 51 1.00
149 0 378 0 0 378 0.00 1.00 0.00 0.00 T 51 1.00
150 0 4 717 0 721 0.00 0.01 0.99 0.00 G 51 0.99
151 0 618 2 0 620 0.00 1.00 0.00 0.00 T 61 1.00
152 0 843 0 0 843 0.00 1.00 0.00 0.00 T 61 1.00
153 0 753 0 0 753 0.00 1.00 0.00 0.00 T 61 1.00
154 0 710 0 0 710 0.00 1.00 0.00 0.00 T 58 1.00
155 0 3 1 782 786 0.00 0.00 0.00 0.99 C 58 0.99
156 0 0 431 3 434 0.00 0.00 0.99 0.01 G 58 0.99
157 0 0 792 0 792 0.00 0.00 1.00 0.00 G 61 1.00
158 0 0 559 0 559 0.00 0.00 1.00 0.00 G 58 1.00
159 0 0 679 0 679 0.00 0.00 1.00 0.00 G 58 1.00
160 0 587 0 0 587 0.00 1.00 0.00 0.00 T 58 1.00
161 0 761 0 0 761 0.00 1.00 0.00 0.00 T 51 1.00
162 0 570 0 0 570 0.00 1.00 0.00 0.00 T 51 1.00
163 564 0 0 0 564 1.00 0.00 0.00 0.00 A 58 1.00
164 0 688 0 0 688 0.00 1.00 0.00 0.00 T 61 1.00
165 0 424 0 0 424 0.00 1.00 0.00 0.00 T 61 1.00
166 0 757 2 0 759 0.00 1.00 0.00 0.00 T 61 1.00
167 0 0 1055 0 1055 0.00 0.00 1.00 0.00 G 58 1.00
168 0 0 387 0 387 0.00 0.00 1.00 0.00 G 58 1.00
169 0 446 1 0 447 0.00 1.00 0.00 0.00 T 51 1.00
170 0 810 3 0 813 0.00 1.00 0.00 0.00 T 51 1.00
171 0 5 981 0 986 0.00 0.01 0.99 0.00 G 58 0.99
172 0 398 2 0 400 0.00 1.00 0.00 0.00 T 58 1.00
173 604 2 0 0 606 1.00 0.00 0.00 0.00 A 58 1.00
174 0 0 330 0 330 0.00 0.00 1.00 0.00 G 58 1.00
175 0 516 1 0 517 0.00 1.00 0.00 0.00 T 58 1.00
176 2 681 0 0 683 0.00 1.00 0.00 0.00 T 61 1.00
177 491 2 0 1 494 0.99 0.00 0.00 0.00 A 61 0.99
178 2 0 0 625 627 0.00 0.00 0.00 1.00 C 58 1.00
179 0 0 438 2 440 0.00 0.00 1.00 0.00 G 58 1.00
180 2 511 0 0 513 0.00 1.00 0.00 0.00 T 58 1.00
181 643 3 0 0 646 1.00 0.00 0.00 0.00 A 61 1.00
182 2 628 0 0 630 0.00 1.00 0.00 0.00 T 61 1.00
183 0 822 0 0 822 0.00 1.00 0.00 0.00 T 61 1.00
184 0 769 0 0 769 0.00 1.00 0.00 0.00 T 61 1.00
185 0 804 0 0 804 0.00 1.00 0.00 0.00 T 61 1.00
186 0 784 0 0 784 0.00 1.00 0.00 0.00 T 61 1.00
187 0 785 0 0 785 0.00 1.00 0.00 0.00 T 61 1.00
188 0 808 0 0 808 0.00 1.00 0.00 0.00 T 61 1.00
189 0 780 0 0 780 0.00 1.00 0.00 0.00 T 58 1.00
190 8 583 0 0 591 0.01 0.99 0.00 0.00 T 28 0.99
191 472 0 0 0 472 1.00 0.00 0.00 0.00 A 58 1.00
192 91 0 399 0 490 0.19 0.00 0.81 0.00 G 32 0.81
193 0 351 139 0 490 0.00 0.72 0.28 0.00 T 32 0.72
194 0 2 388 0 390 0.00 0.01 0.99 0.00 G 58 0.99
195 0 0 380 2 382 0.00 0.00 0.99 0.01 G 58 0.99
196 0 0 22 350 372 0.00 0.00 0.06 0.94 C 58 0.94
197 0 0 415 6 421 0.00 0.00 0.99 0.01 G 58 0.99
198 0 315 0 91 406 0.00 0.78 0.00 0.22 T 34 0.78
199 0 0 1 592 593 0.00 0.00 0.00 1.00 C 58 1.00
200 0 0 306 0 306 0.00 0.00 1.00 0.00 G 58 1.00
201 112 0 503 0 615 0.18 0.00 0.82 0.00 G 34 0.82
202 544 0 0 3 547 0.99 0.00 0.00 0.01 A 46 0.99
203 370 0 0 0 370 1.00 0.00 0.00 0.00 A 32 1.00
204 0 384 0 0 384 0.00 1.00 0.00 0.00 T 51 1.00
205 0 657 15 0 672 0.00 0.98 0.02 0.00 T 58 0.98
206 0 6 713 0 719 0.00 0.01 0.99 0.00 G 58 0.99
207 14 272 7 0 293 0.05 0.93 0.02 0.00 T 58 0.93
208 398 0 0 0 398 1.00 0.00 0.00 0.00 A 58 1.00
209 363 0 0 0 363 1.00 0.00 0.00 0.00 A 58 1.00
210 334 0 71 0 405 0.82 0.00 0.18 0.00 A 34 0.82
211 10 0 412 0 422 0.02 0.00 0.98 0.00 G 58 0.98
212 28 262 0 0 290 0.10 0.90 0.00 0.00 T 51 0.90
213 478 7 0 0 485 0.99 0.01 0.00 0.00 A 46 0.99
214 1 496 0 0 497 0.00 1.00 0.00 0.00 T 51 1.00
215 0 641 0 0 641 0.00 1.00 0.00 0.00 T 58 1.00
216 0 550 24 0 574 0.00 0.96 0.04 0.00 T 58 0.96
217 0 10 627 0 637 0.00 0.02 0.98 0.00 G 51 0.98
218 0 297 131 0 428 0.00 0.69 0.31 0.00 T 32 0.69
219 32 0 607 0 639 0.05 0.00 0.95 0.00 G 51 0.95
220 700 0 13 0 713 0.98 0.00 0.02 0.00 A 58 0.98
221 2 122 507 0 631 0.00 0.19 0.80 0.00 G 34 0.80
222 0 495 0 0 495 0.00 1.00 0.00 0.00 T 58 1.00
223 0 658 0 0 658 0.00 1.00 0.00 0.00 T 58 1.00
224 0 476 0 29 505 0.00 0.94 0.00 0.06 T 58 0.94
225 0 2 0 634 636 0.00 0.00 0.00 1.00 C 58 1.00
226 0 2 0 444 446 0.00 0.00 0.00 1.00 C 58 1.00
227 0 450 0 43 493 0.00 0.91 0.00 0.09 T 58 0.91
228 0 2 0 673 675 0.00 0.00 0.00 1.00 C 58 1.00
229 70 0 285 5 360 0.19 0.00 0.79 0.01 G 32 0.79
230 401 0 0 18 419 0.96 0.00 0.00 0.04 A 32 0.96
231 1 69 0 341 411 0.00 0.17 0.00 0.83 C 31 0.83
232 0 540 228 0 768 0.00 0.70 0.30 0.00 T 26 0.70
233 0 5 601 0 606 0.00 0.01 0.99 0.00 G 27 0.99
234 0 296 211 0 507 0.00 0.58 0.42 0.00 T 25 0.58
235 0 1 588 7 596 0.00 0.00 0.99 0.01 G 28 0.99
236 0 0 3 296 299 0.00 0.00 0.01 0.99 C 45 0.99
237 0 116 0 560 676 0.00 0.17 0.00 0.83 C 31 0.83
238 3 576 0 0 579 0.01 0.99 0.00 0.00 T 46 0.99
239 141 554 0 32 727 0.19 0.76 0.00 0.04 T 30 0.76
240 31 38 0 616 685 0.05 0.06 0.00 0.90 C 26 0.90
241 294 404 0 0 698 0.42 0.58 0.00 0.00 T 17 0.58
242 1233 1 0 0 1234 1.00 0.00 0.00 0.00 A 27 1.00
243 780 0 0 0 780 1.00 0.00 0.00 0.00 A 36 1.00
244 110 0 0 0 110 1.00 0.00 0.00 0.00 A 25 1.00

Quality report

Trimming thresholds :

  • Trimming Method : M1
  • Minimum base error probability : 0.001 %
  • Minimum Phred quality score : 30
Raw sequence information Values
Raw sequence length : 244 bp
Mean of raw sequence Phred quality scores : 42.34
Quality report - Trimmed sequence information Values
Trimmed sequence length : 204 bp
Trimmed sequence start position : 27
Trimmed sequence end position : 231
Mean of trimmed sequence Phred quality scores : 46.75

Mixed base peak report

Trimming thresholds :

  • Minimum primary peak ratio for a position to be considered non-mixed : 0.75
  • Minimum of non-mixed positions percentage in the trimmed sequence to be considered non-mixed : 75 %
  • Minimum number of consecutive non-mixed positions at extremities to get a non-mixed positions percentage above threshold for the trimmed sequence (computed) : 3 bp
Raw sequence information Values
Raw sequence length : 244 bp
Mean of raw sequence primary peak ratios : 0.94
Percentage of non-mixed positions on raw sequence : 88.52 %
Mixed peak report - Trimmed sequence information Values
Trimmed sequence length : 244 bp
Trimmed sequence start position : 1
Trimmed sequence end position : 244
Mean of trimmed sequence primary peak ratios : 0.94
Percentage of non-mixed positions on trimmed sequence : 88.52 %

Trimming plot

Final trimmed sequence

Sequence
Final trimmed sequence information Values
Length : 205 bp
Start position : 27
End position : 231
Mean of Phred quality scores : 46.68
Mean of primary peak ratio : 0.94
Percentage of non-mixed positions : 89.27 %

Sequence of primary peaks:

## GTTTTGCGTTGTGCGAAGGGCGGGTGGGCGGGCCGTTGGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTTCCTCGAC
Chromatogram

Open chromatogram file in a new tab

Table
Position A peak T peak G peak C peak Total A ratio T ratio G ratio C ratio Primary base Quality score Primary ratio
27 0 2 2368 0 2370 0.00 0.00 1.00 0.00 G 33 1.00
28 2 2342 2 0 2346 0.00 1.00 0.00 0.00 T 20 1.00
29 1619 1818 0 0 3437 0.47 0.53 0.00 0.00 T 17 0.53
30 0 2202 0 0 2202 0.00 1.00 0.00 0.00 T 17 1.00
31 3 1323 0 580 1906 0.00 0.69 0.00 0.30 T 16 0.69
32 0 0 2518 0 2518 0.00 0.00 1.00 0.00 G 26 1.00
33 0 0 0 627 627 0.00 0.00 0.00 1.00 C 34 1.00
34 0 0 931 0 931 0.00 0.00 1.00 0.00 G 35 1.00
35 0 1617 0 0 1617 0.00 1.00 0.00 0.00 T 34 1.00
36 0 1901 3 0 1904 0.00 1.00 0.00 0.00 T 29 1.00
37 1579 0 2296 0 3875 0.41 0.00 0.59 0.00 G 24 0.59
38 0 1177 0 0 1177 0.00 1.00 0.00 0.00 T 27 1.00
39 0 1 796 0 797 0.00 0.00 1.00 0.00 G 16 1.00
40 610 0 0 707 1317 0.46 0.00 0.00 0.54 C 16 0.54
41 0 0 786 1 787 0.00 0.00 1.00 0.00 G 27 1.00
42 712 192 0 0 904 0.79 0.21 0.00 0.00 A 22 0.79
43 497 0 364 0 861 0.58 0.00 0.42 0.00 A 14 0.58
44 0 607 871 0 1478 0.00 0.41 0.59 0.00 G 12 0.59
45 0 0 2 0 2 0.00 0.00 1.00 0.00 G 21 1.00
46 0 0 2 0 2 0.00 0.00 1.00 0.00 G 18 1.00
47 0 349 1 860 1210 0.00 0.29 0.00 0.71 C 19 0.71
48 0 2 979 2 983 0.00 0.00 1.00 0.00 G 26 1.00
49 0 130 715 0 845 0.00 0.15 0.85 0.00 G 35 0.85
50 0 0 757 0 757 0.00 0.00 1.00 0.00 G 29 1.00
51 0 428 0 0 428 0.00 1.00 0.00 0.00 T 27 1.00
52 202 0 797 0 999 0.20 0.00 0.80 0.00 G 26 0.80
53 0 0 696 0 696 0.00 0.00 1.00 0.00 G 36 1.00
54 0 172 388 0 560 0.00 0.31 0.69 0.00 G 33 0.69
55 0 129 0 664 793 0.00 0.16 0.00 0.84 C 36 0.84
56 0 0 730 282 1012 0.00 0.00 0.72 0.28 G 25 0.72
57 0 1 741 349 1091 0.00 0.00 0.68 0.32 G 15 0.68
58 0 285 304 0 589 0.00 0.48 0.52 0.00 G 14 0.52
59 0 462 1 467 930 0.00 0.50 0.00 0.50 C 14 0.50
60 1 0 0 981 982 0.00 0.00 0.00 1.00 C 26 1.00
61 192 0 489 0 681 0.28 0.00 0.72 0.00 G 26 0.72
62 0 302 1 148 451 0.00 0.67 0.00 0.33 T 15 0.67
63 0 1241 1 1 1243 0.00 1.00 0.00 0.00 T 26 1.00
64 444 0 542 0 986 0.45 0.00 0.55 0.00 G 15 0.55
65 0 187 658 0 845 0.00 0.22 0.78 0.00 G 25 0.78
66 0 483 226 0 709 0.00 0.68 0.32 0.00 T 16 0.68
67 0 994 2 337 1333 0.00 0.75 0.00 0.25 T 16 0.75
68 0 772 0 0 772 0.00 1.00 0.00 0.00 T 40 1.00
69 0 416 0 994 1410 0.00 0.30 0.00 0.70 C 29 0.70
70 0 0 327 2 329 0.00 0.00 0.99 0.01 G 25 0.99
71 0 422 0 308 730 0.00 0.58 0.00 0.42 T 16 0.58
72 1 1294 0 0 1295 0.00 1.00 0.00 0.00 T 26 1.00
73 589 703 0 0 1292 0.46 0.54 0.00 0.00 T 15 0.54
74 622 921 1 0 1544 0.40 0.60 0.00 0.00 T 15 0.60
75 0 3 1242 0 1245 0.00 0.00 1.00 0.00 G 26 1.00
76 46 0 404 0 450 0.10 0.00 0.90 0.00 G 51 0.90
77 0 0 630 0 630 0.00 0.00 1.00 0.00 G 51 1.00
78 2 0 644 0 646 0.00 0.00 1.00 0.00 G 29 1.00
79 893 0 0 0 893 1.00 0.00 0.00 0.00 A 29 1.00
80 1 0 668 0 669 0.00 0.00 1.00 0.00 G 46 1.00
81 1 0 970 0 971 0.00 0.00 1.00 0.00 G 58 1.00
82 0 0 798 0 798 0.00 0.00 1.00 0.00 G 61 1.00
83 0 0 726 0 726 0.00 0.00 1.00 0.00 G 61 1.00
84 0 756 0 0 756 0.00 1.00 0.00 0.00 T 61 1.00
85 0 914 0 0 914 0.00 1.00 0.00 0.00 T 61 1.00
86 0 3 2 1071 1076 0.00 0.00 0.00 1.00 C 58 1.00
87 0 0 652 0 652 0.00 0.00 1.00 0.00 G 58 1.00
88 0 0 4 807 811 0.00 0.00 0.00 1.00 C 58 1.00
89 0 0 1138 0 1138 0.00 0.00 1.00 0.00 G 58 1.00
90 0 799 3 0 802 0.00 1.00 0.00 0.00 T 58 1.00
91 0 854 0 0 854 0.00 1.00 0.00 0.00 T 58 1.00
92 0 3 1047 0 1050 0.00 0.00 1.00 0.00 G 51 1.00
93 0 605 2 0 607 0.00 1.00 0.00 0.00 T 58 1.00
94 0 912 2 0 914 0.00 1.00 0.00 0.00 T 58 1.00
95 0 2 1004 0 1006 0.00 0.00 1.00 0.00 G 58 1.00
96 842 1 2 0 845 1.00 0.00 0.00 0.00 A 58 1.00
97 1 696 0 0 697 0.00 1.00 0.00 0.00 T 51 1.00
98 0 958 1 0 959 0.00 1.00 0.00 0.00 T 51 1.00
99 0 4 1226 0 1230 0.00 0.00 1.00 0.00 G 41 1.00
100 0 2 565 0 567 0.00 0.00 1.00 0.00 G 51 1.00
101 0 518 0 0 518 0.00 1.00 0.00 0.00 T 51 1.00
102 0 957 3 0 960 0.00 1.00 0.00 0.00 T 51 1.00
103 0 5 1344 0 1349 0.00 0.00 1.00 0.00 G 58 1.00
104 0 530 0 0 530 0.00 1.00 0.00 0.00 T 61 1.00
105 0 2 1294 0 1296 0.00 0.00 1.00 0.00 G 61 1.00
106 0 2 675 0 677 0.00 0.00 1.00 0.00 G 51 1.00
107 0 479 0 1 480 0.00 1.00 0.00 0.00 T 58 1.00
108 0 2 0 991 993 0.00 0.00 0.00 1.00 C 51 1.00
109 0 0 659 2 661 0.00 0.00 1.00 0.00 G 58 1.00
110 0 0 757 0 757 0.00 0.00 1.00 0.00 G 51 1.00
111 2 421 1 0 424 0.00 0.99 0.00 0.00 T 51 0.99
112 733 1 1 0 735 1.00 0.00 0.00 0.00 A 51 1.00
113 0 0 435 0 435 0.00 0.00 1.00 0.00 G 46 1.00
114 0 2 845 0 847 0.00 0.00 1.00 0.00 G 58 1.00
115 0 524 0 0 524 0.00 1.00 0.00 0.00 T 58 1.00
116 4 0 871 0 875 0.00 0.00 1.00 0.00 G 58 1.00
117 840 0 2 0 842 1.00 0.00 0.00 0.00 A 58 1.00
118 657 0 0 0 657 1.00 0.00 0.00 0.00 A 58 1.00
119 1 758 0 0 759 0.00 1.00 0.00 0.00 T 46 1.00
120 0 1165 0 0 1165 0.00 1.00 0.00 0.00 T 51 1.00
121 0 962 0 0 962 0.00 1.00 0.00 0.00 T 51 1.00
122 0 906 0 0 906 0.00 1.00 0.00 0.00 T 58 1.00
123 0 759 0 0 759 0.00 1.00 0.00 0.00 T 61 1.00
124 849 2 2 0 853 1.00 0.00 0.00 0.00 A 58 1.00
125 0 2 620 0 622 0.00 0.00 1.00 0.00 G 58 1.00
126 0 639 0 0 639 0.00 1.00 0.00 0.00 T 51 1.00
127 3 808 0 0 811 0.00 1.00 0.00 0.00 T 58 1.00
128 639 2 0 0 641 1.00 0.00 0.00 0.00 A 51 1.00
129 547 2 0 0 549 1.00 0.00 0.00 0.00 A 51 1.00
130 2 685 0 0 687 0.00 1.00 0.00 0.00 T 51 1.00
131 2 957 0 0 959 0.00 1.00 0.00 0.00 T 51 1.00
132 792 3 2 0 797 0.99 0.00 0.00 0.00 A 51 0.99
133 3 0 693 0 696 0.00 0.00 1.00 0.00 G 58 1.00
134 0 0 0 528 528 0.00 0.00 0.00 1.00 C 58 1.00
135 0 0 880 2 882 0.00 0.00 1.00 0.00 G 58 1.00
136 0 0 566 0 566 0.00 0.00 1.00 0.00 G 58 1.00
137 2 534 1 0 537 0.00 0.99 0.00 0.00 T 51 0.99
138 655 0 0 0 655 1.00 0.00 0.00 0.00 A 51 1.00
139 1 0 1 599 601 0.00 0.00 0.00 1.00 C 41 1.00
140 0 0 482 0 482 0.00 0.00 1.00 0.00 G 58 1.00
141 0 0 879 0 879 0.00 0.00 1.00 0.00 G 58 1.00
142 0 0 583 0 583 0.00 0.00 1.00 0.00 G 58 1.00
143 0 0 685 0 685 0.00 0.00 1.00 0.00 G 58 1.00
144 0 0 722 0 722 0.00 0.00 1.00 0.00 G 58 1.00
145 0 0 716 2 718 0.00 0.00 1.00 0.00 G 61 1.00
146 0 0 4 536 540 0.00 0.00 0.01 0.99 C 61 0.99
147 0 0 872 2 874 0.00 0.00 1.00 0.00 G 58 1.00
148 0 0 679 0 679 0.00 0.00 1.00 0.00 G 51 1.00
149 0 378 0 0 378 0.00 1.00 0.00 0.00 T 51 1.00
150 0 4 717 0 721 0.00 0.01 0.99 0.00 G 51 0.99
151 0 618 2 0 620 0.00 1.00 0.00 0.00 T 61 1.00
152 0 843 0 0 843 0.00 1.00 0.00 0.00 T 61 1.00
153 0 753 0 0 753 0.00 1.00 0.00 0.00 T 61 1.00
154 0 710 0 0 710 0.00 1.00 0.00 0.00 T 58 1.00
155 0 3 1 782 786 0.00 0.00 0.00 0.99 C 58 0.99
156 0 0 431 3 434 0.00 0.00 0.99 0.01 G 58 0.99
157 0 0 792 0 792 0.00 0.00 1.00 0.00 G 61 1.00
158 0 0 559 0 559 0.00 0.00 1.00 0.00 G 58 1.00
159 0 0 679 0 679 0.00 0.00 1.00 0.00 G 58 1.00
160 0 587 0 0 587 0.00 1.00 0.00 0.00 T 58 1.00
161 0 761 0 0 761 0.00 1.00 0.00 0.00 T 51 1.00
162 0 570 0 0 570 0.00 1.00 0.00 0.00 T 51 1.00
163 564 0 0 0 564 1.00 0.00 0.00 0.00 A 58 1.00
164 0 688 0 0 688 0.00 1.00 0.00 0.00 T 61 1.00
165 0 424 0 0 424 0.00 1.00 0.00 0.00 T 61 1.00
166 0 757 2 0 759 0.00 1.00 0.00 0.00 T 61 1.00
167 0 0 1055 0 1055 0.00 0.00 1.00 0.00 G 58 1.00
168 0 0 387 0 387 0.00 0.00 1.00 0.00 G 58 1.00
169 0 446 1 0 447 0.00 1.00 0.00 0.00 T 51 1.00
170 0 810 3 0 813 0.00 1.00 0.00 0.00 T 51 1.00
171 0 5 981 0 986 0.00 0.01 0.99 0.00 G 58 0.99
172 0 398 2 0 400 0.00 1.00 0.00 0.00 T 58 1.00
173 604 2 0 0 606 1.00 0.00 0.00 0.00 A 58 1.00
174 0 0 330 0 330 0.00 0.00 1.00 0.00 G 58 1.00
175 0 516 1 0 517 0.00 1.00 0.00 0.00 T 58 1.00
176 2 681 0 0 683 0.00 1.00 0.00 0.00 T 61 1.00
177 491 2 0 1 494 0.99 0.00 0.00 0.00 A 61 0.99
178 2 0 0 625 627 0.00 0.00 0.00 1.00 C 58 1.00
179 0 0 438 2 440 0.00 0.00 1.00 0.00 G 58 1.00
180 2 511 0 0 513 0.00 1.00 0.00 0.00 T 58 1.00
181 643 3 0 0 646 1.00 0.00 0.00 0.00 A 61 1.00
182 2 628 0 0 630 0.00 1.00 0.00 0.00 T 61 1.00
183 0 822 0 0 822 0.00 1.00 0.00 0.00 T 61 1.00
184 0 769 0 0 769 0.00 1.00 0.00 0.00 T 61 1.00
185 0 804 0 0 804 0.00 1.00 0.00 0.00 T 61 1.00
186 0 784 0 0 784 0.00 1.00 0.00 0.00 T 61 1.00
187 0 785 0 0 785 0.00 1.00 0.00 0.00 T 61 1.00
188 0 808 0 0 808 0.00 1.00 0.00 0.00 T 61 1.00
189 0 780 0 0 780 0.00 1.00 0.00 0.00 T 58 1.00
190 8 583 0 0 591 0.01 0.99 0.00 0.00 T 28 0.99
191 472 0 0 0 472 1.00 0.00 0.00 0.00 A 58 1.00
192 91 0 399 0 490 0.19 0.00 0.81 0.00 G 32 0.81
193 0 351 139 0 490 0.00 0.72 0.28 0.00 T 32 0.72
194 0 2 388 0 390 0.00 0.01 0.99 0.00 G 58 0.99
195 0 0 380 2 382 0.00 0.00 0.99 0.01 G 58 0.99
196 0 0 22 350 372 0.00 0.00 0.06 0.94 C 58 0.94
197 0 0 415 6 421 0.00 0.00 0.99 0.01 G 58 0.99
198 0 315 0 91 406 0.00 0.78 0.00 0.22 T 34 0.78
199 0 0 1 592 593 0.00 0.00 0.00 1.00 C 58 1.00
200 0 0 306 0 306 0.00 0.00 1.00 0.00 G 58 1.00
201 112 0 503 0 615 0.18 0.00 0.82 0.00 G 34 0.82
202 544 0 0 3 547 0.99 0.00 0.00 0.01 A 46 0.99
203 370 0 0 0 370 1.00 0.00 0.00 0.00 A 32 1.00
204 0 384 0 0 384 0.00 1.00 0.00 0.00 T 51 1.00
205 0 657 15 0 672 0.00 0.98 0.02 0.00 T 58 0.98
206 0 6 713 0 719 0.00 0.01 0.99 0.00 G 58 0.99
207 14 272 7 0 293 0.05 0.93 0.02 0.00 T 58 0.93
208 398 0 0 0 398 1.00 0.00 0.00 0.00 A 58 1.00
209 363 0 0 0 363 1.00 0.00 0.00 0.00 A 58 1.00
210 334 0 71 0 405 0.82 0.00 0.18 0.00 A 34 0.82
211 10 0 412 0 422 0.02 0.00 0.98 0.00 G 58 0.98
212 28 262 0 0 290 0.10 0.90 0.00 0.00 T 51 0.90
213 478 7 0 0 485 0.99 0.01 0.00 0.00 A 46 0.99
214 1 496 0 0 497 0.00 1.00 0.00 0.00 T 51 1.00
215 0 641 0 0 641 0.00 1.00 0.00 0.00 T 58 1.00
216 0 550 24 0 574 0.00 0.96 0.04 0.00 T 58 0.96
217 0 10 627 0 637 0.00 0.02 0.98 0.00 G 51 0.98
218 0 297 131 0 428 0.00 0.69 0.31 0.00 T 32 0.69
219 32 0 607 0 639 0.05 0.00 0.95 0.00 G 51 0.95
220 700 0 13 0 713 0.98 0.00 0.02 0.00 A 58 0.98
221 2 122 507 0 631 0.00 0.19 0.80 0.00 G 34 0.80
222 0 495 0 0 495 0.00 1.00 0.00 0.00 T 58 1.00
223 0 658 0 0 658 0.00 1.00 0.00 0.00 T 58 1.00
224 0 476 0 29 505 0.00 0.94 0.00 0.06 T 58 0.94
225 0 2 0 634 636 0.00 0.00 0.00 1.00 C 58 1.00
226 0 2 0 444 446 0.00 0.00 0.00 1.00 C 58 1.00
227 0 450 0 43 493 0.00 0.91 0.00 0.09 T 58 0.91
228 0 2 0 673 675 0.00 0.00 0.00 1.00 C 58 1.00
229 70 0 285 5 360 0.19 0.00 0.79 0.01 G 32 0.79
230 401 0 0 18 419 0.96 0.00 0.00 0.04 A 32 0.96
231 1 69 0 341 411 0.00 0.17 0.00 0.83 C 31 0.83

Sequencing result #2

Raw sequence

Sequence

Sequence of primary peaks:

Length: 228 bp 

## AAATAAATTCCATAGCCCTCTAACCTTAATTACTATCACCCTCTTAGTAGAGGGTTAATTACCGCCCCCCGTACCGCTAATTAACTAAAAATTCACCTACCGACCACAACCAATCAACAACGCGAACCCCTCCCCAAAACGAAACTAACGACCCGCCCACCCGACCTCGCATAAACGCGATAACCCTCTAACCTAAAATTACTAAACCCTTTAGTGAGGGTTAATTAA
Chromatogram

Open chromatogram file in a new tab

Table
Position A peak T peak G peak C peak Total A ratio T ratio G ratio C ratio Primary base Quality score Primary ratio
1 1957 0 0 1545 3502 0.56 0.00 0.00 0.44 A 5 0.56
2 1737 839 0 483 3059 0.57 0.27 0.00 0.16 A 2 0.57
3 957 0 0 474 1431 0.67 0.00 0.00 0.33 A 12 0.67
4 0 1586 0 0 1586 0.00 1.00 0.00 0.00 T 10 1.00
5 2332 1251 0 0 3583 0.65 0.35 0.00 0.00 A 11 0.65
6 2346 0 0 436 2782 0.84 0.00 0.00 0.16 A 11 0.84
7 2018 0 0 0 2018 1.00 0.00 0.00 0.00 A 35 1.00
8 0 1153 0 0 1153 0.00 1.00 0.00 0.00 T 55 1.00
9 0 1656 0 0 1656 0.00 1.00 0.00 0.00 T 55 1.00
10 0 0 0 1460 1460 0.00 0.00 0.00 1.00 C 52 1.00
11 0 0 0 1115 1115 0.00 0.00 0.00 1.00 C 20 1.00
12 1118 0 282 1 1401 0.80 0.00 0.20 0.00 A 5 0.80
13 0 328 2 1 331 0.00 0.99 0.01 0.00 T 19 0.99
14 1014 0 0 292 1306 0.78 0.00 0.00 0.22 A 8 0.78
15 0 1 383 0 384 0.00 0.00 1.00 0.00 G 9 1.00
16 0 0 1 1425 1426 0.00 0.00 0.00 1.00 C 20 1.00
17 0 0 0 1400 1400 0.00 0.00 0.00 1.00 C 47 1.00
18 0 0 0 1115 1115 0.00 0.00 0.00 1.00 C 52 1.00
19 2 1171 0 0 1173 0.00 1.00 0.00 0.00 T 25 1.00
20 495 0 0 924 1419 0.35 0.00 0.00 0.65 C 9 0.65
21 0 393 4 1 398 0.00 0.99 0.01 0.00 T 9 0.99
22 1359 1 0 0 1360 1.00 0.00 0.00 0.00 A 45 1.00
23 1106 0 0 0 1106 1.00 0.00 0.00 0.00 A 40 1.00
24 0 0 0 547 547 0.00 0.00 0.00 1.00 C 30 1.00
25 206 0 0 714 920 0.22 0.00 0.00 0.78 C 14 0.78
26 0 548 0 1 549 0.00 1.00 0.00 0.00 T 30 1.00
27 0 241 0 0 241 0.00 1.00 0.00 0.00 T 11 1.00
28 889 1 0 0 890 1.00 0.00 0.00 0.00 A 16 1.00
29 869 1 0 188 1058 0.82 0.00 0.00 0.18 A 40 0.82
30 0 655 0 0 655 0.00 1.00 0.00 0.00 T 47 1.00
31 0 1008 173 0 1181 0.00 0.85 0.15 0.00 T 52 0.85
32 1102 0 0 1 1103 1.00 0.00 0.00 0.00 A 52 1.00
33 0 1 0 642 643 0.00 0.00 0.00 1.00 C 52 1.00
34 0 559 0 0 559 0.00 1.00 0.00 0.00 T 20 1.00
35 753 0 0 336 1089 0.69 0.00 0.00 0.31 A 9 0.69
36 0 467 0 0 467 0.00 1.00 0.00 0.00 T 9 1.00
37 0 0 0 1 1 0.00 0.00 0.00 1.00 C 30 1.00
38 1017 0 0 0 1017 1.00 0.00 0.00 0.00 A 32 1.00
39 2 0 0 1218 1220 0.00 0.00 0.00 1.00 C 40 1.00
40 206 0 0 741 947 0.22 0.00 0.00 0.78 C 25 0.78
41 0 1 0 840 841 0.00 0.00 0.00 1.00 C 25 1.00
42 0 824 0 0 824 0.00 1.00 0.00 0.00 T 30 1.00
43 0 0 0 256 256 0.00 0.00 0.00 1.00 C 22 1.00
44 233 1145 0 0 1378 0.17 0.83 0.00 0.00 T 22 0.83
45 581 794 0 0 1375 0.42 0.58 0.00 0.00 T 19 0.58
46 1370 0 0 0 1370 1.00 0.00 0.00 0.00 A 20 1.00
47 0 0 318 0 318 0.00 0.00 1.00 0.00 G 5 1.00
48 0 403 0 0 403 0.00 1.00 0.00 0.00 T 3 1.00
49 572 519 6 0 1097 0.52 0.47 0.01 0.00 A 5 0.52
50 233 2 352 0 587 0.40 0.00 0.60 0.00 G 20 0.60
51 1578 0 0 0 1578 1.00 0.00 0.00 0.00 A 23 1.00
52 2 0 1136 694 1832 0.00 0.00 0.62 0.38 G 19 0.62
53 0 0 1308 617 1925 0.00 0.00 0.68 0.32 G 21 0.68
54 0 1 845 557 1403 0.00 0.00 0.60 0.40 G 11 0.60
55 0 684 0 548 1232 0.00 0.56 0.00 0.44 T 10 0.56
56 0 627 501 0 1128 0.00 0.56 0.44 0.00 T 19 0.56
57 1453 0 0 0 1453 1.00 0.00 0.00 0.00 A 14 1.00
58 1297 0 0 0 1297 1.00 0.00 0.00 0.00 A 45 1.00
59 370 956 0 0 1326 0.28 0.72 0.00 0.00 T 40 0.72
60 0 2626 0 0 2626 0.00 1.00 0.00 0.00 T 22 1.00
61 4900 6 0 295 5201 0.94 0.00 0.00 0.06 A 20 0.94
62 151 0 0 437 588 0.26 0.00 0.00 0.74 C 10 0.74
63 0 0 0 537 537 0.00 0.00 0.00 1.00 C 20 1.00
64 0 0 626 19 645 0.00 0.00 0.97 0.03 G 45 0.97
65 0 0 0 621 621 0.00 0.00 0.00 1.00 C 45 1.00
66 0 0 0 871 871 0.00 0.00 0.00 1.00 C 55 1.00
67 0 0 0 811 811 0.00 0.00 0.00 1.00 C 55 1.00
68 0 0 0 901 901 0.00 0.00 0.00 1.00 C 55 1.00
69 0 0 0 792 792 0.00 0.00 0.00 1.00 C 55 1.00
70 0 0 0 707 707 0.00 0.00 0.00 1.00 C 52 1.00
71 0 0 711 0 711 0.00 0.00 1.00 0.00 G 52 1.00
72 0 396 0 0 396 0.00 1.00 0.00 0.00 T 23 1.00
73 686 0 0 0 686 1.00 0.00 0.00 0.00 A 45 1.00
74 1 0 0 752 753 0.00 0.00 0.00 1.00 C 45 1.00
75 0 0 0 697 697 0.00 0.00 0.00 1.00 C 52 1.00
76 0 0 798 30 828 0.00 0.00 0.96 0.04 G 52 0.96
77 0 0 0 511 511 0.00 0.00 0.00 1.00 C 45 1.00
78 0 614 0 1 615 0.00 1.00 0.00 0.00 T 45 1.00
79 641 0 0 0 641 1.00 0.00 0.00 0.00 A 52 1.00
80 683 0 0 0 683 1.00 0.00 0.00 0.00 A 52 1.00
81 0 579 0 0 579 0.00 1.00 0.00 0.00 T 55 1.00
82 0 788 0 0 788 0.00 1.00 0.00 0.00 T 55 1.00
83 777 1 0 0 778 1.00 0.00 0.00 0.00 A 52 1.00
84 481 0 0 0 481 1.00 0.00 0.00 0.00 A 52 1.00
85 0 0 0 477 477 0.00 0.00 0.00 1.00 C 52 1.00
86 0 576 0 0 576 0.00 1.00 0.00 0.00 T 52 1.00
87 744 0 0 0 744 1.00 0.00 0.00 0.00 A 55 1.00
88 548 0 0 0 548 1.00 0.00 0.00 0.00 A 52 1.00
89 511 0 0 0 511 1.00 0.00 0.00 0.00 A 52 1.00
90 690 0 0 0 690 1.00 0.00 0.00 0.00 A 45 1.00
91 569 0 0 0 569 1.00 0.00 0.00 0.00 A 40 1.00
92 1 670 0 0 671 0.00 1.00 0.00 0.00 T 45 1.00
93 0 826 0 0 826 0.00 1.00 0.00 0.00 T 52 1.00
94 1 2 0 697 700 0.00 0.00 0.00 1.00 C 52 1.00
95 363 0 0 0 363 1.00 0.00 0.00 0.00 A 52 1.00
96 0 0 0 625 625 0.00 0.00 0.00 1.00 C 52 1.00
97 0 4 0 719 723 0.00 0.01 0.00 0.99 C 52 0.99
98 0 651 0 3 654 0.00 1.00 0.00 0.00 T 45 1.00
99 823 0 0 2 825 1.00 0.00 0.00 0.00 A 45 1.00
100 2 0 0 652 654 0.00 0.00 0.00 1.00 C 45 1.00
101 0 0 8 607 615 0.00 0.00 0.01 0.99 C 35 0.99
102 0 0 767 3 770 0.00 0.00 1.00 0.00 G 35 1.00
103 932 0 2 2 936 1.00 0.00 0.00 0.00 A 45 1.00
104 1 0 0 644 645 0.00 0.00 0.00 1.00 C 52 1.00
105 0 0 0 621 621 0.00 0.00 0.00 1.00 C 52 1.00
106 506 0 0 5 511 0.99 0.00 0.00 0.01 A 52 0.99
107 2 0 0 540 542 0.00 0.00 0.00 1.00 C 55 1.00
108 473 0 0 2 475 1.00 0.00 0.00 0.00 A 52 1.00
109 541 0 0 2 543 1.00 0.00 0.00 0.00 A 52 1.00
110 2 0 0 584 586 0.00 0.00 0.00 1.00 C 52 1.00
111 1 0 0 650 651 0.00 0.00 0.00 1.00 C 45 1.00
112 538 0 0 2 540 1.00 0.00 0.00 0.00 A 45 1.00
113 565 0 0 0 565 1.00 0.00 0.00 0.00 A 52 1.00
114 0 523 0 0 523 0.00 1.00 0.00 0.00 T 45 1.00
115 0 2 0 775 777 0.00 0.00 0.00 1.00 C 45 1.00
116 494 0 0 2 496 1.00 0.00 0.00 0.00 A 52 1.00
117 459 0 0 0 459 1.00 0.00 0.00 0.00 A 52 1.00
118 6 0 0 488 494 0.01 0.00 0.00 0.99 C 52 0.99
119 537 0 0 2 539 1.00 0.00 0.00 0.00 A 52 1.00
120 496 0 0 2 498 1.00 0.00 0.00 0.00 A 52 1.00
121 0 0 7 554 561 0.00 0.00 0.01 0.99 C 45 0.99
122 0 0 624 4 628 0.00 0.00 0.99 0.01 G 45 0.99
123 0 0 22 615 637 0.00 0.00 0.03 0.97 C 40 0.97
124 3 0 498 2 503 0.01 0.00 0.99 0.00 G 40 0.99
125 715 0 0 0 715 1.00 0.00 0.00 0.00 A 40 1.00
126 859 0 0 0 859 1.00 0.00 0.00 0.00 A 52 1.00
127 0 0 0 709 709 0.00 0.00 0.00 1.00 C 52 1.00
128 0 0 0 892 892 0.00 0.00 0.00 1.00 C 55 1.00
129 0 0 0 972 972 0.00 0.00 0.00 1.00 C 52 1.00
130 0 5 0 808 813 0.00 0.01 0.00 0.99 C 52 0.99
131 0 756 0 35 791 0.00 0.96 0.00 0.04 T 52 0.96
132 0 1 0 1035 1036 0.00 0.00 0.00 1.00 C 52 1.00
133 0 0 0 876 876 0.00 0.00 0.00 1.00 C 52 1.00
134 0 0 0 812 812 0.00 0.00 0.00 1.00 C 52 1.00
135 1 0 0 689 690 0.00 0.00 0.00 1.00 C 52 1.00
136 537 0 0 2 539 1.00 0.00 0.00 0.00 A 52 1.00
137 577 0 0 0 577 1.00 0.00 0.00 0.00 A 55 1.00
138 715 0 0 0 715 1.00 0.00 0.00 0.00 A 55 1.00
139 669 0 0 0 669 1.00 0.00 0.00 0.00 A 52 1.00
140 0 0 2 481 483 0.00 0.00 0.00 1.00 C 52 1.00
141 143 0 507 2 652 0.22 0.00 0.78 0.00 G 28 0.78
142 657 0 2 0 659 1.00 0.00 0.00 0.00 A 52 1.00
143 831 0 0 0 831 1.00 0.00 0.00 0.00 A 52 1.00
144 573 0 0 0 573 1.00 0.00 0.00 0.00 A 45 1.00
145 1 11 0 578 590 0.00 0.02 0.00 0.98 C 45 0.98
146 0 640 0 0 640 0.00 1.00 0.00 0.00 T 45 1.00
147 863 2 0 0 865 1.00 0.00 0.00 0.00 A 45 1.00
148 639 0 0 0 639 1.00 0.00 0.00 0.00 A 52 1.00
149 0 0 25 514 539 0.00 0.00 0.05 0.95 C 45 0.95
150 25 0 674 2 701 0.04 0.00 0.96 0.00 G 40 0.96
151 783 0 2 2 787 0.99 0.00 0.00 0.00 A 35 0.99
152 2 0 0 722 724 0.00 0.00 0.00 1.00 C 45 1.00
153 0 0 0 856 856 0.00 0.00 0.00 1.00 C 52 1.00
154 0 0 3 860 863 0.00 0.00 0.00 1.00 C 52 1.00
155 0 0 711 28 739 0.00 0.00 0.96 0.04 G 52 0.96
156 0 0 2 691 693 0.00 0.00 0.00 1.00 C 52 1.00
157 0 0 0 980 980 0.00 0.00 0.00 1.00 C 52 1.00
158 0 0 0 808 808 0.00 0.00 0.00 1.00 C 52 1.00
159 555 0 0 43 598 0.93 0.00 0.00 0.07 A 52 0.93
160 0 0 0 758 758 0.00 0.00 0.00 1.00 C 52 1.00
161 0 0 0 844 844 0.00 0.00 0.00 1.00 C 52 1.00
162 0 0 0 807 807 0.00 0.00 0.00 1.00 C 45 1.00
163 140 0 667 2 809 0.17 0.00 0.82 0.00 G 25 0.82
164 957 0 0 2 959 1.00 0.00 0.00 0.00 A 40 1.00
165 1 0 0 679 680 0.00 0.00 0.00 1.00 C 45 1.00
166 0 6 0 791 797 0.00 0.01 0.00 0.99 C 52 0.99
167 0 623 0 57 680 0.00 0.92 0.00 0.08 T 52 0.92
168 0 1 0 967 968 0.00 0.00 0.00 1.00 C 52 1.00
169 0 0 483 31 514 0.00 0.00 0.94 0.06 G 52 0.94
170 4 0 0 502 506 0.01 0.00 0.00 0.99 C 45 0.99
171 568 9 0 0 577 0.98 0.02 0.00 0.00 A 52 0.98
172 64 534 0 0 598 0.11 0.89 0.00 0.00 T 52 0.89
173 903 2 0 0 905 1.00 0.00 0.00 0.00 A 52 1.00
174 634 0 0 0 634 1.00 0.00 0.00 0.00 A 52 1.00
175 477 0 0 0 477 1.00 0.00 0.00 0.00 A 45 1.00
176 0 0 7 596 603 0.00 0.00 0.01 0.99 C 45 0.99
177 0 0 570 27 597 0.00 0.00 0.95 0.05 G 52 0.95
178 0 0 27 686 713 0.00 0.00 0.04 0.96 C 52 0.96
179 20 0 534 0 554 0.04 0.00 0.96 0.00 G 45 0.96
180 718 0 0 0 718 1.00 0.00 0.00 0.00 A 45 1.00
181 0 477 0 0 477 0.00 1.00 0.00 0.00 T 52 1.00
182 791 2 0 0 793 1.00 0.00 0.00 0.00 A 52 1.00
183 602 0 0 2 604 1.00 0.00 0.00 0.00 A 52 1.00
184 0 0 0 769 769 0.00 0.00 0.00 1.00 C 52 1.00
185 0 0 0 955 955 0.00 0.00 0.00 1.00 C 52 1.00
186 0 5 0 795 800 0.00 0.01 0.00 0.99 C 52 0.99
187 0 662 0 47 709 0.00 0.93 0.00 0.07 T 52 0.93
188 0 23 0 860 883 0.00 0.03 0.00 0.97 C 52 0.97
189 0 518 0 2 520 0.00 1.00 0.00 0.00 T 52 1.00
190 843 0 0 0 843 1.00 0.00 0.00 0.00 A 52 1.00
191 550 0 0 2 552 1.00 0.00 0.00 0.00 A 52 1.00
192 2 0 0 640 642 0.00 0.00 0.00 1.00 C 52 1.00
193 0 3 0 730 733 0.00 0.00 0.00 1.00 C 52 1.00
194 0 511 0 0 511 0.00 1.00 0.00 0.00 T 52 1.00
195 794 2 0 0 796 1.00 0.00 0.00 0.00 A 52 1.00
196 561 0 0 0 561 1.00 0.00 0.00 0.00 A 52 1.00
197 568 0 0 0 568 1.00 0.00 0.00 0.00 A 52 1.00
198 621 11 0 0 632 0.98 0.02 0.00 0.00 A 52 0.98
199 4 718 0 0 722 0.01 0.99 0.00 0.00 T 52 0.99
200 46 808 0 0 854 0.05 0.95 0.00 0.00 T 52 0.95
201 794 3 0 0 797 1.00 0.00 0.00 0.00 A 52 1.00
202 3 4 0 596 603 0.00 0.01 0.00 0.99 C 52 0.99
203 155 485 0 2 642 0.24 0.76 0.00 0.00 T 26 0.76
204 835 2 0 0 837 1.00 0.00 0.00 0.00 A 45 1.00
205 596 0 0 0 596 1.00 0.00 0.00 0.00 A 45 1.00
206 441 0 0 97 538 0.82 0.00 0.00 0.18 A 26 0.82
207 2 0 0 643 645 0.00 0.00 0.00 1.00 C 52 1.00
208 0 0 0 846 846 0.00 0.00 0.00 1.00 C 52 1.00
209 0 22 0 717 739 0.00 0.03 0.00 0.97 C 52 0.97
210 0 749 0 0 749 0.00 1.00 0.00 0.00 T 52 1.00
211 18 953 0 0 971 0.02 0.98 0.00 0.00 T 52 0.98
212 96 661 0 0 757 0.13 0.87 0.00 0.00 T 52 0.87
213 763 0 0 0 763 1.00 0.00 0.00 0.00 A 52 1.00
214 142 4 567 0 713 0.20 0.01 0.80 0.00 G 23 0.80
215 0 406 313 0 719 0.00 0.56 0.44 0.00 T 19 0.56
216 41 0 485 0 526 0.08 0.00 0.92 0.00 G 35 0.92
217 540 0 267 0 807 0.67 0.00 0.33 0.00 A 19 0.67
218 1 0 807 0 808 0.00 0.00 1.00 0.00 G 35 1.00
219 0 0 1037 0 1037 0.00 0.00 1.00 0.00 G 45 1.00
220 0 5 685 0 690 0.00 0.01 0.99 0.00 G 45 0.99
221 0 567 1 0 568 0.00 1.00 0.00 0.00 T 52 1.00
222 242 553 0 0 795 0.30 0.70 0.00 0.00 T 28 0.70
223 886 2 0 0 888 1.00 0.00 0.00 0.00 A 52 1.00
224 733 170 0 0 903 0.81 0.19 0.00 0.00 A 28 0.81
225 105 951 0 0 1056 0.10 0.90 0.00 0.00 T 23 0.90
226 1002 1905 0 0 2907 0.34 0.66 0.00 0.00 T 19 0.66
227 3827 8 0 0 3835 1.00 0.00 0.00 0.00 A 20 1.00
228 380 0 0 0 380 1.00 0.00 0.00 0.00 A 25 1.00

Quality report

Trimming thresholds :

  • Trimming Method : M1
  • Minimum base error probability : 0.001 %
  • Minimum Phred quality score : 30
Raw sequence information Values
Raw sequence length : 228 bp
Mean of raw sequence Phred quality scores : 40.9
Quality report - Trimmed sequence information Values
Trimmed sequence length : 206 bp
Trimmed sequence start position : 7
Trimmed sequence end position : 213
Mean of trimmed sequence Phred quality scores : 42.58

Mixed base peak report

Trimming thresholds :

  • Minimum primary peak ratio for a position to be considered non-mixed : 0.75
  • Minimum of non-mixed positions percentage in the trimmed sequence to be considered non-mixed : 75 %
  • Minimum number of consecutive non-mixed positions at extremities to get a non-mixed positions percentage above threshold for the trimmed sequence (computed) : 3 bp
Raw sequence information Values
Raw sequence length : 228 bp
Mean of raw sequence primary peak ratios : 0.95
Percentage of non-mixed positions on raw sequence : 91.23 %
Mixed peak report - Trimmed sequence information Values
Trimmed sequence length : 220 bp
Trimmed sequence start position : 6
Trimmed sequence end position : 225
Mean of trimmed sequence primary peak ratios : 0.96
Percentage of non-mixed positions on trimmed sequence : 93.18 %

Trimming plot

Final trimmed sequence

Sequence
Final trimmed sequence information Values
Length : 207 bp
Start position : 7
End position : 213
Mean of Phred quality scores : 42.54
Mean of primary peak ratio : 0.96
Percentage of non-mixed positions : 94.2 %

Sequence of primary peaks:

## ATTCCATAGCCCTCTAACCTTAATTACTATCACCCTCTTAGTAGAGGGTTAATTACCGCCCCCCGTACCGCTAATTAACTAAAAATTCACCTACCGACCACAACCAATCAACAACGCGAACCCCTCCCCAAAACGAAACTAACGACCCGCCCACCCGACCTCGCATAAACGCGATAACCCTCTAACCTAAAATTACTAAACCCTTTA
Chromatogram

Open chromatogram file in a new tab

Table
Position A peak T peak G peak C peak Total A ratio T ratio G ratio C ratio Primary base Quality score Primary ratio
7 2018 0 0 0 2018 1.00 0.00 0.00 0.00 A 35 1.00
8 0 1153 0 0 1153 0.00 1.00 0.00 0.00 T 55 1.00
9 0 1656 0 0 1656 0.00 1.00 0.00 0.00 T 55 1.00
10 0 0 0 1460 1460 0.00 0.00 0.00 1.00 C 52 1.00
11 0 0 0 1115 1115 0.00 0.00 0.00 1.00 C 20 1.00
12 1118 0 282 1 1401 0.80 0.00 0.20 0.00 A 5 0.80
13 0 328 2 1 331 0.00 0.99 0.01 0.00 T 19 0.99
14 1014 0 0 292 1306 0.78 0.00 0.00 0.22 A 8 0.78
15 0 1 383 0 384 0.00 0.00 1.00 0.00 G 9 1.00
16 0 0 1 1425 1426 0.00 0.00 0.00 1.00 C 20 1.00
17 0 0 0 1400 1400 0.00 0.00 0.00 1.00 C 47 1.00
18 0 0 0 1115 1115 0.00 0.00 0.00 1.00 C 52 1.00
19 2 1171 0 0 1173 0.00 1.00 0.00 0.00 T 25 1.00
20 495 0 0 924 1419 0.35 0.00 0.00 0.65 C 9 0.65
21 0 393 4 1 398 0.00 0.99 0.01 0.00 T 9 0.99
22 1359 1 0 0 1360 1.00 0.00 0.00 0.00 A 45 1.00
23 1106 0 0 0 1106 1.00 0.00 0.00 0.00 A 40 1.00
24 0 0 0 547 547 0.00 0.00 0.00 1.00 C 30 1.00
25 206 0 0 714 920 0.22 0.00 0.00 0.78 C 14 0.78
26 0 548 0 1 549 0.00 1.00 0.00 0.00 T 30 1.00
27 0 241 0 0 241 0.00 1.00 0.00 0.00 T 11 1.00
28 889 1 0 0 890 1.00 0.00 0.00 0.00 A 16 1.00
29 869 1 0 188 1058 0.82 0.00 0.00 0.18 A 40 0.82
30 0 655 0 0 655 0.00 1.00 0.00 0.00 T 47 1.00
31 0 1008 173 0 1181 0.00 0.85 0.15 0.00 T 52 0.85
32 1102 0 0 1 1103 1.00 0.00 0.00 0.00 A 52 1.00
33 0 1 0 642 643 0.00 0.00 0.00 1.00 C 52 1.00
34 0 559 0 0 559 0.00 1.00 0.00 0.00 T 20 1.00
35 753 0 0 336 1089 0.69 0.00 0.00 0.31 A 9 0.69
36 0 467 0 0 467 0.00 1.00 0.00 0.00 T 9 1.00
37 0 0 0 1 1 0.00 0.00 0.00 1.00 C 30 1.00
38 1017 0 0 0 1017 1.00 0.00 0.00 0.00 A 32 1.00
39 2 0 0 1218 1220 0.00 0.00 0.00 1.00 C 40 1.00
40 206 0 0 741 947 0.22 0.00 0.00 0.78 C 25 0.78
41 0 1 0 840 841 0.00 0.00 0.00 1.00 C 25 1.00
42 0 824 0 0 824 0.00 1.00 0.00 0.00 T 30 1.00
43 0 0 0 256 256 0.00 0.00 0.00 1.00 C 22 1.00
44 233 1145 0 0 1378 0.17 0.83 0.00 0.00 T 22 0.83
45 581 794 0 0 1375 0.42 0.58 0.00 0.00 T 19 0.58
46 1370 0 0 0 1370 1.00 0.00 0.00 0.00 A 20 1.00
47 0 0 318 0 318 0.00 0.00 1.00 0.00 G 5 1.00
48 0 403 0 0 403 0.00 1.00 0.00 0.00 T 3 1.00
49 572 519 6 0 1097 0.52 0.47 0.01 0.00 A 5 0.52
50 233 2 352 0 587 0.40 0.00 0.60 0.00 G 20 0.60
51 1578 0 0 0 1578 1.00 0.00 0.00 0.00 A 23 1.00
52 2 0 1136 694 1832 0.00 0.00 0.62 0.38 G 19 0.62
53 0 0 1308 617 1925 0.00 0.00 0.68 0.32 G 21 0.68
54 0 1 845 557 1403 0.00 0.00 0.60 0.40 G 11 0.60
55 0 684 0 548 1232 0.00 0.56 0.00 0.44 T 10 0.56
56 0 627 501 0 1128 0.00 0.56 0.44 0.00 T 19 0.56
57 1453 0 0 0 1453 1.00 0.00 0.00 0.00 A 14 1.00
58 1297 0 0 0 1297 1.00 0.00 0.00 0.00 A 45 1.00
59 370 956 0 0 1326 0.28 0.72 0.00 0.00 T 40 0.72
60 0 2626 0 0 2626 0.00 1.00 0.00 0.00 T 22 1.00
61 4900 6 0 295 5201 0.94 0.00 0.00 0.06 A 20 0.94
62 151 0 0 437 588 0.26 0.00 0.00 0.74 C 10 0.74
63 0 0 0 537 537 0.00 0.00 0.00 1.00 C 20 1.00
64 0 0 626 19 645 0.00 0.00 0.97 0.03 G 45 0.97
65 0 0 0 621 621 0.00 0.00 0.00 1.00 C 45 1.00
66 0 0 0 871 871 0.00 0.00 0.00 1.00 C 55 1.00
67 0 0 0 811 811 0.00 0.00 0.00 1.00 C 55 1.00
68 0 0 0 901 901 0.00 0.00 0.00 1.00 C 55 1.00
69 0 0 0 792 792 0.00 0.00 0.00 1.00 C 55 1.00
70 0 0 0 707 707 0.00 0.00 0.00 1.00 C 52 1.00
71 0 0 711 0 711 0.00 0.00 1.00 0.00 G 52 1.00
72 0 396 0 0 396 0.00 1.00 0.00 0.00 T 23 1.00
73 686 0 0 0 686 1.00 0.00 0.00 0.00 A 45 1.00
74 1 0 0 752 753 0.00 0.00 0.00 1.00 C 45 1.00
75 0 0 0 697 697 0.00 0.00 0.00 1.00 C 52 1.00
76 0 0 798 30 828 0.00 0.00 0.96 0.04 G 52 0.96
77 0 0 0 511 511 0.00 0.00 0.00 1.00 C 45 1.00
78 0 614 0 1 615 0.00 1.00 0.00 0.00 T 45 1.00
79 641 0 0 0 641 1.00 0.00 0.00 0.00 A 52 1.00
80 683 0 0 0 683 1.00 0.00 0.00 0.00 A 52 1.00
81 0 579 0 0 579 0.00 1.00 0.00 0.00 T 55 1.00
82 0 788 0 0 788 0.00 1.00 0.00 0.00 T 55 1.00
83 777 1 0 0 778 1.00 0.00 0.00 0.00 A 52 1.00
84 481 0 0 0 481 1.00 0.00 0.00 0.00 A 52 1.00
85 0 0 0 477 477 0.00 0.00 0.00 1.00 C 52 1.00
86 0 576 0 0 576 0.00 1.00 0.00 0.00 T 52 1.00
87 744 0 0 0 744 1.00 0.00 0.00 0.00 A 55 1.00
88 548 0 0 0 548 1.00 0.00 0.00 0.00 A 52 1.00
89 511 0 0 0 511 1.00 0.00 0.00 0.00 A 52 1.00
90 690 0 0 0 690 1.00 0.00 0.00 0.00 A 45 1.00
91 569 0 0 0 569 1.00 0.00 0.00 0.00 A 40 1.00
92 1 670 0 0 671 0.00 1.00 0.00 0.00 T 45 1.00
93 0 826 0 0 826 0.00 1.00 0.00 0.00 T 52 1.00
94 1 2 0 697 700 0.00 0.00 0.00 1.00 C 52 1.00
95 363 0 0 0 363 1.00 0.00 0.00 0.00 A 52 1.00
96 0 0 0 625 625 0.00 0.00 0.00 1.00 C 52 1.00
97 0 4 0 719 723 0.00 0.01 0.00 0.99 C 52 0.99
98 0 651 0 3 654 0.00 1.00 0.00 0.00 T 45 1.00
99 823 0 0 2 825 1.00 0.00 0.00 0.00 A 45 1.00
100 2 0 0 652 654 0.00 0.00 0.00 1.00 C 45 1.00
101 0 0 8 607 615 0.00 0.00 0.01 0.99 C 35 0.99
102 0 0 767 3 770 0.00 0.00 1.00 0.00 G 35 1.00
103 932 0 2 2 936 1.00 0.00 0.00 0.00 A 45 1.00
104 1 0 0 644 645 0.00 0.00 0.00 1.00 C 52 1.00
105 0 0 0 621 621 0.00 0.00 0.00 1.00 C 52 1.00
106 506 0 0 5 511 0.99 0.00 0.00 0.01 A 52 0.99
107 2 0 0 540 542 0.00 0.00 0.00 1.00 C 55 1.00
108 473 0 0 2 475 1.00 0.00 0.00 0.00 A 52 1.00
109 541 0 0 2 543 1.00 0.00 0.00 0.00 A 52 1.00
110 2 0 0 584 586 0.00 0.00 0.00 1.00 C 52 1.00
111 1 0 0 650 651 0.00 0.00 0.00 1.00 C 45 1.00
112 538 0 0 2 540 1.00 0.00 0.00 0.00 A 45 1.00
113 565 0 0 0 565 1.00 0.00 0.00 0.00 A 52 1.00
114 0 523 0 0 523 0.00 1.00 0.00 0.00 T 45 1.00
115 0 2 0 775 777 0.00 0.00 0.00 1.00 C 45 1.00
116 494 0 0 2 496 1.00 0.00 0.00 0.00 A 52 1.00
117 459 0 0 0 459 1.00 0.00 0.00 0.00 A 52 1.00
118 6 0 0 488 494 0.01 0.00 0.00 0.99 C 52 0.99
119 537 0 0 2 539 1.00 0.00 0.00 0.00 A 52 1.00
120 496 0 0 2 498 1.00 0.00 0.00 0.00 A 52 1.00
121 0 0 7 554 561 0.00 0.00 0.01 0.99 C 45 0.99
122 0 0 624 4 628 0.00 0.00 0.99 0.01 G 45 0.99
123 0 0 22 615 637 0.00 0.00 0.03 0.97 C 40 0.97
124 3 0 498 2 503 0.01 0.00 0.99 0.00 G 40 0.99
125 715 0 0 0 715 1.00 0.00 0.00 0.00 A 40 1.00
126 859 0 0 0 859 1.00 0.00 0.00 0.00 A 52 1.00
127 0 0 0 709 709 0.00 0.00 0.00 1.00 C 52 1.00
128 0 0 0 892 892 0.00 0.00 0.00 1.00 C 55 1.00
129 0 0 0 972 972 0.00 0.00 0.00 1.00 C 52 1.00
130 0 5 0 808 813 0.00 0.01 0.00 0.99 C 52 0.99
131 0 756 0 35 791 0.00 0.96 0.00 0.04 T 52 0.96
132 0 1 0 1035 1036 0.00 0.00 0.00 1.00 C 52 1.00
133 0 0 0 876 876 0.00 0.00 0.00 1.00 C 52 1.00
134 0 0 0 812 812 0.00 0.00 0.00 1.00 C 52 1.00
135 1 0 0 689 690 0.00 0.00 0.00 1.00 C 52 1.00
136 537 0 0 2 539 1.00 0.00 0.00 0.00 A 52 1.00
137 577 0 0 0 577 1.00 0.00 0.00 0.00 A 55 1.00
138 715 0 0 0 715 1.00 0.00 0.00 0.00 A 55 1.00
139 669 0 0 0 669 1.00 0.00 0.00 0.00 A 52 1.00
140 0 0 2 481 483 0.00 0.00 0.00 1.00 C 52 1.00
141 143 0 507 2 652 0.22 0.00 0.78 0.00 G 28 0.78
142 657 0 2 0 659 1.00 0.00 0.00 0.00 A 52 1.00
143 831 0 0 0 831 1.00 0.00 0.00 0.00 A 52 1.00
144 573 0 0 0 573 1.00 0.00 0.00 0.00 A 45 1.00
145 1 11 0 578 590 0.00 0.02 0.00 0.98 C 45 0.98
146 0 640 0 0 640 0.00 1.00 0.00 0.00 T 45 1.00
147 863 2 0 0 865 1.00 0.00 0.00 0.00 A 45 1.00
148 639 0 0 0 639 1.00 0.00 0.00 0.00 A 52 1.00
149 0 0 25 514 539 0.00 0.00 0.05 0.95 C 45 0.95
150 25 0 674 2 701 0.04 0.00 0.96 0.00 G 40 0.96
151 783 0 2 2 787 0.99 0.00 0.00 0.00 A 35 0.99
152 2 0 0 722 724 0.00 0.00 0.00 1.00 C 45 1.00
153 0 0 0 856 856 0.00 0.00 0.00 1.00 C 52 1.00
154 0 0 3 860 863 0.00 0.00 0.00 1.00 C 52 1.00
155 0 0 711 28 739 0.00 0.00 0.96 0.04 G 52 0.96
156 0 0 2 691 693 0.00 0.00 0.00 1.00 C 52 1.00
157 0 0 0 980 980 0.00 0.00 0.00 1.00 C 52 1.00
158 0 0 0 808 808 0.00 0.00 0.00 1.00 C 52 1.00
159 555 0 0 43 598 0.93 0.00 0.00 0.07 A 52 0.93
160 0 0 0 758 758 0.00 0.00 0.00 1.00 C 52 1.00
161 0 0 0 844 844 0.00 0.00 0.00 1.00 C 52 1.00
162 0 0 0 807 807 0.00 0.00 0.00 1.00 C 45 1.00
163 140 0 667 2 809 0.17 0.00 0.82 0.00 G 25 0.82
164 957 0 0 2 959 1.00 0.00 0.00 0.00 A 40 1.00
165 1 0 0 679 680 0.00 0.00 0.00 1.00 C 45 1.00
166 0 6 0 791 797 0.00 0.01 0.00 0.99 C 52 0.99
167 0 623 0 57 680 0.00 0.92 0.00 0.08 T 52 0.92
168 0 1 0 967 968 0.00 0.00 0.00 1.00 C 52 1.00
169 0 0 483 31 514 0.00 0.00 0.94 0.06 G 52 0.94
170 4 0 0 502 506 0.01 0.00 0.00 0.99 C 45 0.99
171 568 9 0 0 577 0.98 0.02 0.00 0.00 A 52 0.98
172 64 534 0 0 598 0.11 0.89 0.00 0.00 T 52 0.89
173 903 2 0 0 905 1.00 0.00 0.00 0.00 A 52 1.00
174 634 0 0 0 634 1.00 0.00 0.00 0.00 A 52 1.00
175 477 0 0 0 477 1.00 0.00 0.00 0.00 A 45 1.00
176 0 0 7 596 603 0.00 0.00 0.01 0.99 C 45 0.99
177 0 0 570 27 597 0.00 0.00 0.95 0.05 G 52 0.95
178 0 0 27 686 713 0.00 0.00 0.04 0.96 C 52 0.96
179 20 0 534 0 554 0.04 0.00 0.96 0.00 G 45 0.96
180 718 0 0 0 718 1.00 0.00 0.00 0.00 A 45 1.00
181 0 477 0 0 477 0.00 1.00 0.00 0.00 T 52 1.00
182 791 2 0 0 793 1.00 0.00 0.00 0.00 A 52 1.00
183 602 0 0 2 604 1.00 0.00 0.00 0.00 A 52 1.00
184 0 0 0 769 769 0.00 0.00 0.00 1.00 C 52 1.00
185 0 0 0 955 955 0.00 0.00 0.00 1.00 C 52 1.00
186 0 5 0 795 800 0.00 0.01 0.00 0.99 C 52 0.99
187 0 662 0 47 709 0.00 0.93 0.00 0.07 T 52 0.93
188 0 23 0 860 883 0.00 0.03 0.00 0.97 C 52 0.97
189 0 518 0 2 520 0.00 1.00 0.00 0.00 T 52 1.00
190 843 0 0 0 843 1.00 0.00 0.00 0.00 A 52 1.00
191 550 0 0 2 552 1.00 0.00 0.00 0.00 A 52 1.00
192 2 0 0 640 642 0.00 0.00 0.00 1.00 C 52 1.00
193 0 3 0 730 733 0.00 0.00 0.00 1.00 C 52 1.00
194 0 511 0 0 511 0.00 1.00 0.00 0.00 T 52 1.00
195 794 2 0 0 796 1.00 0.00 0.00 0.00 A 52 1.00
196 561 0 0 0 561 1.00 0.00 0.00 0.00 A 52 1.00
197 568 0 0 0 568 1.00 0.00 0.00 0.00 A 52 1.00
198 621 11 0 0 632 0.98 0.02 0.00 0.00 A 52 0.98
199 4 718 0 0 722 0.01 0.99 0.00 0.00 T 52 0.99
200 46 808 0 0 854 0.05 0.95 0.00 0.00 T 52 0.95
201 794 3 0 0 797 1.00 0.00 0.00 0.00 A 52 1.00
202 3 4 0 596 603 0.00 0.01 0.00 0.99 C 52 0.99
203 155 485 0 2 642 0.24 0.76 0.00 0.00 T 26 0.76
204 835 2 0 0 837 1.00 0.00 0.00 0.00 A 45 1.00
205 596 0 0 0 596 1.00 0.00 0.00 0.00 A 45 1.00
206 441 0 0 97 538 0.82 0.00 0.00 0.18 A 26 0.82
207 2 0 0 643 645 0.00 0.00 0.00 1.00 C 52 1.00
208 0 0 0 846 846 0.00 0.00 0.00 1.00 C 52 1.00
209 0 22 0 717 739 0.00 0.03 0.00 0.97 C 52 0.97
210 0 749 0 0 749 0.00 1.00 0.00 0.00 T 52 1.00
211 18 953 0 0 971 0.02 0.98 0.00 0.00 T 52 0.98
212 96 661 0 0 757 0.13 0.87 0.00 0.00 T 52 0.87
213 763 0 0 0 763 1.00 0.00 0.00 0.00 A 52 1.00

Alignments

Sequencing result #1

Sequencing result #1 is aligned on both sense and antisense bisulfite converted DNA sequences to determine the sequencing direction as forward or reverse.

Alignment as forward

Trimmed sequence of primary peaks from sequencing result #1 is aligned with bisulfite converted reference DNA sense sequence

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:37 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 182
## # Identity:     179/182 (98.4%)
## # Similarity:    NA/182 (NA%)
## # Gaps:           0/182 (0.0%)
## # Score: 337.0359
## #
## #
## #=======================================
## 
## P1                17 AGGGCGGGTGGGCGGGCCGT     36
##                      ||| |||||||||||| |||
## S1               108 AGGTCGGGTGGGCGGGTCGT    127
## 
## P1                37 TGGTTTCGTTTTGGGGAGGG     56
##                      | ||||||||||||||||||
## S1               128 TAGTTTCGTTTTGGGGAGGG    147
## 
## P1                57 GTTCGCGTTGTTGATTGGTT     76
##                      ||||||||||||||||||||
## S1               148 GTTCGCGTTGTTGATTGGTT    167
## 
## P1                77 GTGGTCGGTAGGTGAATTTT     96
##                      ||||||||||||||||||||
## S1               168 GTGGTCGGTAGGTGAATTTT    187
## 
## P1                97 TAGTTAATTAGCGGTACGGG    116
##                      ||||||||||||||||||||
## S1               188 TAGTTAATTAGCGGTACGGG    207
## 
## P1               117 GGGCGGTGTTTTCGGGGTTT    136
##                      ||||||||||||||||||||
## S1               208 GGGCGGTGTTTTCGGGGTTT    227
## 
## P1               137 ATTTGGTTGTAGTTACGTAT    156
##                      ||||||||||||||||||||
## S1               228 ATTTGGTTGTAGTTACGTAT    247
## 
## P1               157 TTTTTTTTAGTGGCGTCGGA    176
##                      ||||||||||||||||||||
## S1               248 TTTTTTTTAGTGGCGTCGGA    267
## 
## P1               177 ATTGTAAAGTATTTGTGAGT    196
##                      ||||||||||||||||||||
## S1               268 ATTGTAAAGTATTTGTGAGT    287
## 
## P1               197 TT    198
##                      ||
## S1               288 TT    289
## 
## 
## #---------------------------------------
## #---------------------------------------

Alignment as reverse

Trimmed sequence of primary peaks from sequencing result #1 is aligned with bisulfite converted reference DNA antisense sequence

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:37 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 6
## # Identity:       6/6 (100.0%)
## # Similarity:    NA/6 (NA%)
## # Gaps:           0/6 (0.0%)
## # Score: 11.89054
## #
## #
## #=======================================
## 
## P1               150 TACGTA    155
##                      ||||||
## S1                96 TACGTA    101
## 
## 
## #---------------------------------------
## #---------------------------------------

Direction determination

Sequencing result #1 corresponds to forward direction

Sequencing result #2

Sequencing result #2 is aligned on both sense and antisense bisulfite converted DNA sequences to determine the sequencing direction as forward or reverse.

Alignment as forward

Trimmed sequence of primary peaks from sequencing result #2 is aligned with bisulfite converted reference DNA sense sequence

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:38 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 10
## # Identity:      10/10 (100.0%)
## # Similarity:    NA/10 (NA%)
## # Gaps:           0/10 (0.0%)
## # Score: 19.81756
## #
## #
## #=======================================
## 
## P1                42 TAGAGGGTTA     51
##                      ||||||||||
## S1                85 TAGAGGGTTA     94
## 
## 
## #---------------------------------------
## #---------------------------------------

Alignment as reverse

Trimmed sequence of primary peaks from sequencing result #2 is aligned with bisulfite converted reference DNA antisense sequence

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:38 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 146
## # Identity:     146/146 (100.0%)
## # Similarity:    NA/146 (NA%)
## # Gaps:           0/146 (0.0%)
## # Score: 289.336
## #
## #
## #=======================================
## 
## P1                55 ACCGCCCCCCGTACCGCTAA     74
##                      ||||||||||||||||||||
## S1               128 ACCGCCCCCCGTACCGCTAA    147
## 
## P1                75 TTAACTAAAAATTCACCTAC     94
##                      ||||||||||||||||||||
## S1               148 TTAACTAAAAATTCACCTAC    167
## 
## P1                95 CGACCACAACCAATCAACAA    114
##                      ||||||||||||||||||||
## S1               168 CGACCACAACCAATCAACAA    187
## 
## P1               115 CGCGAACCCCTCCCCAAAAC    134
##                      ||||||||||||||||||||
## S1               188 CGCGAACCCCTCCCCAAAAC    207
## 
## P1               135 GAAACTAACGACCCGCCCAC    154
##                      ||||||||||||||||||||
## S1               208 GAAACTAACGACCCGCCCAC    227
## 
## P1               155 CCGACCTCGCATAAACGCGA    174
##                      ||||||||||||||||||||
## S1               228 CCGACCTCGCATAAACGCGA    247
## 
## P1               175 TAACCCTCTAACCTAAAATT    194
##                      ||||||||||||||||||||
## S1               248 TAACCCTCTAACCTAAAATT    267
## 
## P1               195 ACTAAA    200
##                      ||||||
## S1               268 ACTAAA    273
## 
## 
## #---------------------------------------
## #---------------------------------------

Direction determination

Sequencing result #2 corresponds to reverse direction

Forward

To find nucleotides of reference DNA sequence positions on sequencing result, the trimmed sequence of primary peaks from forward sequencing results is aligned with bisulfite converted reference DNA sense sequence.

Alignment

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:38 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 182
## # Identity:     179/182 (98.4%)
## # Similarity:    NA/182 (NA%)
## # Gaps:           0/182 (0.0%)
## # Score: 337.0359
## #
## #
## #=======================================
## 
## P1                17 AGGGCGGGTGGGCGGGCCGT     36
##                      ||| |||||||||||| |||
## S1               108 AGGTCGGGTGGGCGGGTCGT    127
## 
## P1                37 TGGTTTCGTTTTGGGGAGGG     56
##                      | ||||||||||||||||||
## S1               128 TAGTTTCGTTTTGGGGAGGG    147
## 
## P1                57 GTTCGCGTTGTTGATTGGTT     76
##                      ||||||||||||||||||||
## S1               148 GTTCGCGTTGTTGATTGGTT    167
## 
## P1                77 GTGGTCGGTAGGTGAATTTT     96
##                      ||||||||||||||||||||
## S1               168 GTGGTCGGTAGGTGAATTTT    187
## 
## P1                97 TAGTTAATTAGCGGTACGGG    116
##                      ||||||||||||||||||||
## S1               188 TAGTTAATTAGCGGTACGGG    207
## 
## P1               117 GGGCGGTGTTTTCGGGGTTT    136
##                      ||||||||||||||||||||
## S1               208 GGGCGGTGTTTTCGGGGTTT    227
## 
## P1               137 ATTTGGTTGTAGTTACGTAT    156
##                      ||||||||||||||||||||
## S1               228 ATTTGGTTGTAGTTACGTAT    247
## 
## P1               157 TTTTTTTTAGTGGCGTCGGA    176
##                      ||||||||||||||||||||
## S1               248 TTTTTTTTAGTGGCGTCGGA    267
## 
## P1               177 ATTGTAAAGTATTTGTGAGT    196
##                      ||||||||||||||||||||
## S1               268 ATTGTAAAGTATTTGTGAGT    287
## 
## P1               197 TT    198
##                      ||
## S1               288 TT    289
## 
## 
## #---------------------------------------
## #---------------------------------------

Aligned sequences

Aligned sequence from forward sequencing result (Pattern P1):

Length: 182 bp 

## AGGGCGGGTGGGCGGGCCGTTGGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTT

Aligned sequence from bisulfite converted reference DNA sense sequence (Subject S1):

Length: 182 bp 

## AGGTCGGGTGGGCGGGTCGTTAGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTT

Reverse

To find nucleotides of reference DNA sequence positions on sequencing result, the trimmed sequence of primary peaks from reverse sequencing results is aligned with bisulfite converted reference DNA antisense sequence.

Alignment

## ########################################
## # Program: Biostrings (version 2.64.1), a Bioconductor package
## # Rundate: Fri Jun  9 17:23:38 2023
## ########################################
## #=======================================
## #
## # Aligned_sequences: 2
## # 1: P1
## # 2: S1
## # Matrix: NA
## # Gap_penalty: 14.0
## # Extend_penalty: 4.0
## #
## # Length: 146
## # Identity:     146/146 (100.0%)
## # Similarity:    NA/146 (NA%)
## # Gaps:           0/146 (0.0%)
## # Score: 289.336
## #
## #
## #=======================================
## 
## P1                55 ACCGCCCCCCGTACCGCTAA     74
##                      ||||||||||||||||||||
## S1               128 ACCGCCCCCCGTACCGCTAA    147
## 
## P1                75 TTAACTAAAAATTCACCTAC     94
##                      ||||||||||||||||||||
## S1               148 TTAACTAAAAATTCACCTAC    167
## 
## P1                95 CGACCACAACCAATCAACAA    114
##                      ||||||||||||||||||||
## S1               168 CGACCACAACCAATCAACAA    187
## 
## P1               115 CGCGAACCCCTCCCCAAAAC    134
##                      ||||||||||||||||||||
## S1               188 CGCGAACCCCTCCCCAAAAC    207
## 
## P1               135 GAAACTAACGACCCGCCCAC    154
##                      ||||||||||||||||||||
## S1               208 GAAACTAACGACCCGCCCAC    227
## 
## P1               155 CCGACCTCGCATAAACGCGA    174
##                      ||||||||||||||||||||
## S1               228 CCGACCTCGCATAAACGCGA    247
## 
## P1               175 TAACCCTCTAACCTAAAATT    194
##                      ||||||||||||||||||||
## S1               248 TAACCCTCTAACCTAAAATT    267
## 
## P1               195 ACTAAA    200
##                      ||||||
## S1               268 ACTAAA    273
## 
## 
## #---------------------------------------
## #---------------------------------------

Aligned sequences

Aligned sequence from reverse sequencing result (Pattern P1):

Length: 146 bp 

## ACCGCCCCCCGTACCGCTAATTAACTAAAAATTCACCTACCGACCACAACCAATCAACAACGCGAACCCCTCCCCAAAACGAAACTAACGACCCGCCCACCCGACCTCGCATAAACGCGATAACCCTCTAACCTAAAATTACTAAA

Aligned sequence from bisulfite converted reference DNA antisense sequence (Subject S1):

Length: 146 bp 

## ACCGCCCCCCGTACCGCTAATTAACTAAAAATTCACCTACCGACCACAACCAATCAACAACGCGAACCCCTCCCCAAAACGAAACTAACGACCCGCCCACCCGACCTCGCATAAACGCGATAACCCTCTAACCTAAAATTACTAAA

Quality control

Summary

Thresholds Values
Minimum length of the aligned sequence : 30 bp
Minimum identity percentage of alignment : 75 %
Minimum of bisulfite conversion rate mean : 0.9
Direction Sequencing Length Identity Mismatch Indel in DNA reference Indel in sequencing Mean of conversion rates SD of conversion rates Quality Result
Forward #1 182 98.35 3 0 0 0.98 0.1 Correct
Reverse #2 146 100.00 0 0 0 1.00 0.0 Correct

Mismatch positions

Forward

Positions in trimmed sequencing result Nucleotides in trimmed sequencing result Positions in reference DNA sequence Nucleotides in reference DNA sequence
20 G 111 T
33 C 124 T
38 G 129 A

Reverse

No mismatch positions in reverse alignment.

Insertions/deletions

Forward

No insertion/deletion in forward alignment.

Reverse

No insertion/deletion in reverse alignment.

Conversion rates

Combined

C number Bisulfite conversion rate Forward Bisulfite conversion rate Reverse
20 NA 1.00
21 NA 1.00
22 NA 1.00
23 NA 1.00
24 NA 1.00
25 NA 1.00
26 NA 1.00
27 NA 1.00
28 NA 1.00
29 NA 1.00
30 NaN 1.00
31 0.50 1.00
32 1.00 1.00
33 1.00 1.00
34 1.00 1.00
35 0.58 1.00
36 1.00 1.00
37 1.00 1.00
38 1.00 1.00
39 1.00 1.00
40 1.00 1.00
41 1.00 1.00
42 1.00 1.00
43 1.00 1.00
44 1.00 1.00
45 1.00 1.00
46 1.00 1.00
47 1.00 1.00
48 1.00 1.00
49 1.00 1.00
50 1.00 1.00
51 1.00 NA
52 1.00 NA
53 1.00 NA
54 1.00 NA
55 1.00 NA
56 1.00 NA
57 1.00 NA
58 1.00 NA
59 1.00 NA
60 1.00 NA
61 1.00 NA
62 1.00 NA
63 1.00 NA
64 1.00 NA
65 1.00 NA
66 1.00 NA
67 1.00 NA
68 1.00 NA
69 1.00 NA
70 1.00 NA
71 1.00 NA
72 1.00 NA
73 1.00 NA
74 1.00 NA
75 1.00 NA

Forward

C number Position in reference DNA Position in sequencing result (trimmed) Position in sequencing result (raw) A peak T peak G peak C peak Bisulfite conversion rate
30 111 20 46 0 0 2 0 NaN
31 124 33 59 0 462 1 467 0.50
32 128 37 63 0 1241 1 1 1.00
33 131 40 66 0 483 226 0 1.00
34 133 42 68 0 772 0 0 1.00
35 136 45 71 0 422 0 308 0.58
36 137 46 72 1 1294 0 0 1.00
37 138 47 73 589 703 0 0 1.00
38 150 59 85 0 914 0 0 1.00
39 155 64 90 0 799 3 0 1.00
40 158 67 93 0 605 2 0 1.00
41 166 75 101 0 518 0 0 1.00
42 172 81 107 0 479 0 1 1.00
43 176 85 111 2 421 1 0 1.00
44 184 93 119 1 758 0 0 1.00
45 185 94 120 0 1165 0 0 1.00
46 186 95 121 0 962 0 0 1.00
47 188 97 123 0 759 0 0 1.00
48 191 100 126 0 639 0 0 1.00
49 192 101 127 3 808 0 0 1.00
50 196 105 131 2 957 0 0 1.00
51 216 125 151 0 618 2 0 1.00
52 217 126 152 0 843 0 0 1.00
53 219 128 154 0 710 0 0 1.00
54 225 134 160 0 587 0 0 1.00
55 227 136 162 0 570 0 0 1.00
56 229 138 164 0 688 0 0 1.00
57 230 139 165 0 424 0 0 1.00
58 234 143 169 0 446 1 0 1.00
59 237 146 172 0 398 2 0 1.00
60 240 149 175 0 516 1 0 1.00
61 241 150 176 2 681 0 0 1.00
62 245 154 180 2 511 0 0 1.00
63 247 156 182 2 628 0 0 1.00
64 248 157 183 0 822 0 0 1.00
65 249 158 184 0 769 0 0 1.00
66 250 159 185 0 804 0 0 1.00
67 251 160 186 0 784 0 0 1.00
68 253 162 188 0 808 0 0 1.00
69 255 164 190 8 583 0 0 1.00
70 269 178 204 0 384 0 0 1.00
71 272 181 207 14 272 7 0 1.00
72 277 186 212 28 262 0 0 1.00
73 279 188 214 1 496 0 0 1.00
74 280 189 215 0 641 0 0 1.00
75 287 196 222 0 495 0 0 1.00

Reverse

C number Position in reference DNA Position in sequencing result (trimmed) Position in sequencing result (raw) A peak T peak G peak C peak Bisulfite conversion rate
50 146 73 79 641 0 0 0 1
49 150 77 83 777 1 0 0 1
48 151 78 84 481 0 0 0 1
47 154 81 87 744 0 0 0 1
46 156 83 89 511 0 0 0 1
45 157 84 90 690 0 0 0 1
44 158 85 91 569 0 0 0 1
43 166 93 99 823 0 0 2 1
42 170 97 103 932 0 2 2 1
41 176 103 109 541 0 0 2 1
40 184 111 117 459 0 0 0 1
39 187 114 120 496 0 0 2 1
38 192 119 125 715 0 0 0 1
37 204 131 137 577 0 0 0 1
36 205 132 138 715 0 0 0 1
35 206 133 139 669 0 0 0 1
34 209 136 142 657 0 2 0 1
33 211 138 144 573 0 0 0 1
32 214 141 147 863 2 0 0 1
31 218 145 151 783 0 2 2 1
30 231 158 164 957 0 0 2 1
29 241 168 174 634 0 0 0 1
28 247 174 180 718 0 0 0 1
27 249 176 182 791 2 0 0 1
26 258 185 191 550 0 0 2 1
25 262 189 195 794 2 0 0 1
24 263 190 196 561 0 0 0 1
23 265 192 198 621 11 0 0 1
22 268 195 201 794 3 0 0 1
21 272 199 205 596 0 0 0 1
20 273 200 206 441 0 0 97 1

Maximum aligned sequence

The maximum aligned sequence corresponds to the maximum sequence covered by at least one correct sequencing.

Length of max aligned sequence : 221 bp
Coordinates of max aligned sequence : chr16:68771008-68771228

Maximum aligned sequence (on bisulfite converted sense sequence from the plus strand sequence) :

## TTTAGTAATTTTAGGTTAGAGGGTTATCGCGTTTATGCGAGGTCGGGTGGGCGGGTCGTTAGTTTCGTTTTGGGGAGGGGTTCGCGTTGTTGATTGGTTGTGGTCGGTAGGTGAATTTTTAGTTAATTAGCGGTACGGGGGGCGGTGTTTTCGGGGTTTATTTGGTTGTAGTTACGTATTTTTTTTTAGTGGCGTCGGAATTGTAAAGTATTTGTGAGTTT

Methylation

Combined

CG number Chromosome Start End Methylation Percentage Forward Methylation Percentage Reverse Methylation Percentage Average Methylation Percentage SD
5 chr16 68771035 68771036 NA 96.39 96.390 NA
6 chr16 68771037 68771038 NA 100.00 100.000 NA
7 chr16 68771045 68771046 NA 100.00 100.000 NA
8 chr16 68771051 68771052 71.13 82.65 76.890 8.15
9 chr16 68771059 68771060 83.73 100.00 91.865 11.50
10 chr16 68771064 68771065 100.00 96.42 98.210 2.53
11 chr16 68771073 68771074 70.50 78.00 74.250 5.30
12 chr16 68771090 68771091 99.72 99.40 99.560 0.23
13 chr16 68771092 68771093 100.00 100.00 100.000 0.00
14 chr16 68771112 68771113 99.80 100.00 99.900 0.14
15 chr16 68771138 68771139 100.00 100.00 100.000 0.00
16 chr16 68771143 68771144 100.00 100.00 100.000 0.00
17 chr16 68771150 68771151 100.00 100.00 100.000 0.00
18 chr16 68771159 68771160 99.62 NA 99.620 NA
19 chr16 68771182 68771183 100.00 NA 100.000 NA
20 chr16 68771200 68771201 100.00 NA 100.000 NA
21 chr16 68771203 68771204 100.00 NA 100.000 NA

Forward

CG number Chromosome Start End C position in reference DNA C position in sequencing result (trimmed) C position in sequencing result (raw) A peak T peak G peak C peak Methylation Percentage
8 chr16 68771051 68771052 112 21 47 0 349 1 860 71.13
9 chr16 68771059 68771060 120 29 55 0 129 0 664 83.73
10 chr16 68771064 68771065 125 34 60 1 0 0 981 100.00
11 chr16 68771073 68771074 134 43 69 0 416 0 994 70.50
12 chr16 68771090 68771091 151 60 86 0 3 2 1071 99.72
13 chr16 68771092 68771093 153 62 88 0 0 4 807 100.00
14 chr16 68771112 68771113 173 82 108 0 2 0 991 99.80
15 chr16 68771138 68771139 199 108 134 0 0 0 528 100.00
16 chr16 68771143 68771144 204 113 139 1 0 1 599 100.00
17 chr16 68771150 68771151 211 120 146 0 0 4 536 100.00
18 chr16 68771159 68771160 220 129 155 0 3 1 782 99.62
19 chr16 68771182 68771183 243 152 178 2 0 0 625 100.00
20 chr16 68771200 68771201 261 170 196 0 0 22 350 100.00
21 chr16 68771203 68771204 264 173 199 0 0 1 592 100.00

Reverse

CG number Chromosome Start End G position in reference DNA G position in sequencing result (trimmed) G position in sequencing result (raw) A peak T peak G peak C peak Methylation Percentage
17 chr16 68771150 68771151 131 58 64 0 0 626 19 100.00
16 chr16 68771143 68771144 138 65 71 0 0 711 0 100.00
15 chr16 68771138 68771139 143 70 76 0 0 798 30 100.00
14 chr16 68771112 68771113 169 96 102 0 0 767 3 100.00
13 chr16 68771092 68771093 189 116 122 0 0 624 4 100.00
12 chr16 68771090 68771091 191 118 124 3 0 498 2 99.40
11 chr16 68771073 68771074 208 135 141 143 0 507 2 78.00
10 chr16 68771064 68771065 217 144 150 25 0 674 2 96.42
9 chr16 68771059 68771060 222 149 155 0 0 711 28 100.00
8 chr16 68771051 68771052 230 157 163 140 0 667 2 82.65
7 chr16 68771045 68771046 236 163 169 0 0 483 31 100.00
6 chr16 68771037 68771038 244 171 177 0 0 570 27 100.00
5 chr16 68771035 68771036 246 173 179 20 0 534 0 96.39

Individual methylation plot

Output data

Directories

Files

Methylation data file preview

CG_nb chromosome start end meth_F meth_R meth_avg meth_sd collection group rep clone alg_coord_start alg_coord_end
5 chr16 68771035 68771036 NA 96.39 96.390 NA High methylated DNA 3 NA 68771008 68771228
6 chr16 68771037 68771038 NA 100.00 100.000 NA High methylated DNA 3 NA 68771008 68771228
7 chr16 68771045 68771046 NA 100.00 100.000 NA High methylated DNA 3 NA 68771008 68771228
8 chr16 68771051 68771052 71.13 82.65 76.890 8.15 High methylated DNA 3 NA 68771008 68771228
9 chr16 68771059 68771060 83.73 100.00 91.865 11.50 High methylated DNA 3 NA 68771008 68771228
10 chr16 68771064 68771065 100.00 96.42 98.210 2.53 High methylated DNA 3 NA 68771008 68771228
11 chr16 68771073 68771074 70.50 78.00 74.250 5.30 High methylated DNA 3 NA 68771008 68771228
12 chr16 68771090 68771091 99.72 99.40 99.560 0.23 High methylated DNA 3 NA 68771008 68771228
13 chr16 68771092 68771093 100.00 100.00 100.000 0.00 High methylated DNA 3 NA 68771008 68771228
14 chr16 68771112 68771113 99.80 100.00 99.900 0.14 High methylated DNA 3 NA 68771008 68771228
15 chr16 68771138 68771139 100.00 100.00 100.000 0.00 High methylated DNA 3 NA 68771008 68771228
16 chr16 68771143 68771144 100.00 100.00 100.000 0.00 High methylated DNA 3 NA 68771008 68771228
17 chr16 68771150 68771151 100.00 100.00 100.000 0.00 High methylated DNA 3 NA 68771008 68771228
18 chr16 68771159 68771160 99.62 NA 99.620 NA High methylated DNA 3 NA 68771008 68771228
19 chr16 68771182 68771183 100.00 NA 100.000 NA High methylated DNA 3 NA 68771008 68771228
20 chr16 68771200 68771201 100.00 NA 100.000 NA High methylated DNA 3 NA 68771008 68771228
21 chr16 68771203 68771204 100.00 NA 100.000 NA High methylated DNA 3 NA 68771008 68771228